


TRON: New Frontiers

by Azaelynn



Category: Star Trek, Star Trek: Alternate Original Series (Movies), Tron (Movies), Tron - All Media Types
Genre: Angst and Feels, Character Death, Eventual Romance, Eventual Smut, M/M, Major Character Injury, Mild Hurt/Comfort, Post-Star Trek: Into Darkness, Romance
Language: English
Status: In-Progress
Published: 2020-06-30
Updated: 2021-02-02
Packaged: 2021-03-04 21:40:18
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 9
Words: 51,116
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/25003279
Author URL: https://archiveofourown.org/users/Azaelynn/pseuds/Azaelynn
Summary: The world wasn't ready for Flynn's miracle. When circumstances force Sam back into the Grid, trapped and alone, how will he cope when once he's finally released, the world he knows is gone? Will he be able to find a kindred soul in Jim Kirk?
Relationships: Minor or Background Relationship(s), Sam Flynn/Tron
Comments: 19
Kudos: 64





	1. Chapter 1

**Author's Note:**

> This is a rewrite of a fic I posted ages ago on ff.net. 
> 
> I started writing this because not long after watching Tron Legacy, I had this vision of both Jim Kirk and Sam Flynn sitting in a bar, swapping stories and basically being the best of buds. I have nothing more than this vision, so it wasn't surprising that the original fic stalled, so here I am, trying to fix that.
> 
> Here's hoping.

A spray of bullets slammed into the brick wall of the old run down building he was running past, showering him with dust and grit. He threw his hands up to protect his face even as a larger chip skimmed past his face, leaving a stinging cut below his eye. He didn't stop running or slow down; he couldn't, so he just ducked into another derelict alley as he used his mental map to try and lose their pursuers, cursing loudly and colorfully as more bullets peppered their steps.

Fuck this shit; this was supposed to happen this way!

The industrial zone they were in was littered with thousands of little side streets and alleys that backtracked and cut off into dead ends, most of which was undocumented in city plans, which meant that if you didn't know where you were going, it was super easy to lose your way. Which was lucky for Sam since he'd spent his days as a kid learning all the ways he could get to his destination.

Bursting out of the alleyway, he quickly pulled Alan down to duck behind an old long broken down truck as a couple blocks away, a heavily armored military humvee crawled down another abandoned street. He waited just a few seconds after the humvee disappeared from view to drag Alan down another side street, ignoring the boarded up doors and windows of the long abandoned store fronts.

"We don't have a lot of time!" Alan said behind him, panting slightly as he raced along with Sam through the empty alleys. "They're gonna know sooner or later where we're going!"

"I know!" Sam vaulted over a low chain link fence, pausing only long enough to help the older man over the top. "We're almost there, and I've been leading them away from the arcade!"

He barely turned the next corner when Alan snatched the back of his leather jacket and pulled him into a ridiculously narrow hole in the wall behind an overfilled dumpster, pressing up against him with one hand covering his mouth and covering his body with his own. Sam could only watch as moments later, a half dozen men stormed through the alley, armed to the absolute teeth, but Alan kept them hidden in the inky darkness of their dilapidated shelter.

It was several long minutes before Alan eased off of Sam, carefully peeking out into the alley for any signs of life. "They're branching out. We should hurry."

The older man grabbed Sam's wrist and pulled him along as he led the way this time, twisting them around in the industrial maze until finally, they reached their destination, the last bastion of hope they had.

Sam moved past Alan to unlock the employee back door of the old arcade his dad owned all those years ago. It was in this place where he could say that everything, good and bad, had started.

It was dark on the inside, with boarded up windows and large dusty plastic sheets covering up the old game machines, dirty and grimy and just as he left it almost two years, after his first, and last visit to the pinnacle of his father's genius, The Grid. The old arcade looked like nothing had touched it in years, nothing had been disturbed, and for that reason alone, Sam felt a touch of relief.

"Why aren't they already here? Shouldn't this be the first place they'd think we'd go?" He asked quietly, watching as Alan kept them away from the windows, keeping them to the shadows of the back wall, hidden by rows of dead machines.

"This was one of your dad's more paranoid decisions, but after he closed the arcade and went full time with Encom, he sold the property to a dummy corporation that I own through my wife's maiden name, and since she's been dead for years, bless her soul, it's still largely unconnected to me." Alan led them to the bare bones kitchen in the corner of the old building, where they were able to take a few minutes to relax and breathe. "Under that corporation, I was able to make it look like construction had started to demolish. It's kept everyone away from here for years."

"Which is why no one's questioned why this place has sat empty these twenty years, 'cause there's no business here anymore." Sam concluded, and yeah, he agreed with Alan about his dad's paranoia. "It also allowed him free access anytime he needed to come here, to work on The Grid."

"Exactly. I may not have understood his reasoning, but I still supported him whenever I could." Alan said it so nonchalantly, like it was no big deal, but Sam felt a pang of fondness in his chest, grateful as always that Alan was there to support him. Despite the tumultuous events of the past thirty six hours, he was stunned the older man, whom he viewed like a father over the long years, was still with him, and freely helping to keep him alive and safe.

Sam was surprised at how capable Alan was; the man was in his early fifties but he was still fit and fast like a man thirty years younger, and with a spy-like stealth and skills that had allowed them to escape past the multiple mercenary groups coming after their heads.

Sam knew that without Alan at his side, he'd have been caught in the first couple, likely at his old home where he'd been dumbstruck by the raging inferno that consumed his house, and likely, his dog.

Sorrow churned his guts at the thought of his little French bulldog Marv dying in the flames. Little guy hadn't deserved that.

Thoughts of his now dead dog led him back to the start of his flight to escape, where he'd stood in shock at the entryways of one of Encom's new medical research labs, where beyond a locked contamination barrier, Quorra had died surrounded by Edward Dillinger and his merc troops, sightless eyes staring at him as a trickle of blood dripped from the hole in her skull.

Alan had saved him there too, drawn in by the SOS from Quorra and he'd managed to completely lock down the research wing, trapping Dillinger inside and allowing them precious time to find out what that bastard had been doing and also succeeding into wiping most of their research and data from Encom's computers.

The world hadn't been ready for the advancements he'd worked so hard these last two years. All Sam had wanted from the marvels gained from Quorra and her ISO DNA was inspired by his dad rewriting her code inside The Grid when she'd almost died defending him. The advances he could bring into the world through bioengineering alone was astounding, let alone the quantum leaps he could make through the application of the digital world and what was available there.

Quorra had stood by his side the entire time, graciously allowing Sam to tinker with sample of her genetic makeup as they made leaps and bounds in the medical field; but that wasn't all... the technology embedded in Quorra's DNA had started to pave the way major advancements in software development, online security, engineering and quantum mechanics, to name a few fields. Everything Sam touched seemed blessed to progress rapidly to the next level, to all the things his dad had told him about as a kid _(bio-digital jazz, man)_... and now, before they'd even managed a step forward to progress, it was all gone.

Sam hadn't like Dillinger as a person, never had, but he could respect the man as a talented code and software developer. The man had worked hard to get past the tainted name by means of his thief father, and when Sam had taken over Encom with more interest, he'd even apologized for his last New Years stunt. He hadn't fully trusted Dillinger, especially when he started making noises about military contracts and weapons development, but he was talented and it'd be a waste to get rid of him simply based on personal bias.

Too bad that decision had backfired in his face.

Sam supposed that he should have seen some of this coming, since Dillinger, right from the start, had been suspicious of Quorra and her origins, since she'd popped up out of nowhere, and had been better than almost of them. Quorra had adapted to life outside The Grid astonishingly quickly, but there had been a few hiccups.

Still, the sight of her lifeless body slumped over the lab console, staring at him with those dead eyes he'd only seen once before with Dillinger standing over her with a gun in his hand was something he was never going to be able to forget.

That had been a day and a half ago, although it seemed like an eternity ago and he and Alan had been running since. But they were running out of places to go and he wasn't really sure how much longer they could keep running.

"Sam. Sam!"

Sam blinked rapidly, Alan's voice cutting through the memories and he breathed deeply, dragging his focus back to reality and their current hopeless situation.

Alan softened around the edges, a look of understanding easing the lines of his faces. "I know it's hard, especially now, but I need you here with me. Show me how to get to your dad's lab."

"Yeah, ok." Alan was right, Sam couldn't get lost inside his own head, he had to stay on point or they both end up captured or dead. He led Alan back through the front of the arcade, to the back wall where the ancient Tron console stood, pushing the machine aside to reveal the hidden he'd stumbled upon so long ago now.

Alan pushed open the door, peering into the darkened stairway, almost completely indistinguishable in the gloom of the old arcade. Sam watched as ideas came and went as Alan considered their options, considering they didn't have a lot of time. He nodded once, muttering as he looked around them sharply, keen eyes taking in the rest of the building. Alan had a plan already, and Sam was keen to get started.

"Alan?" He spoke in barely a whisper, far too loud in the silence."What's the plan?"

"Help me unplug all of the machines. Then we're turning the power on," Sam hurried to comply, confident that Alan would let him know the details as they went. "Then I want your butt down there in that lab."

Sam was already halfway down the line of machines, unplugging the old consoles before moving on to the lighted signs and displays. "What for?"

"When you told me about the Grid, you said your father explained that time moved differently; that hours or days in the Grid was only minutes out here." Alan finished his task and made his way to a supply closet tucked away near the kitchen. "You also told me how dangerous it was in there."

"What of it?"

"The time dilation's not a surprise, since computers operate faster than we do, but if the computer is as advanced as you said it was, would you be able to reverse the dilation? To make so that hours here would only last minutes in there? Seconds, even?"

A part of Alan's developing plan was starting to come to light in Sam's mind, and it filled him with both excitement and trepidation. "Sure, I'd have to write a modded version of that quantum entanglement based communications program we were doing for NASA, the one they wanted for future spaceflights, but yeah, it's doable. It's one of the last things I was working on at Encom, before this whole mess started. I even have the files for it."

"Good," Alan flicked the switch to the power, and luckily only a small barely heard hum was the only indication that there was any activity inside the arcade. "I want you to get down and get started on that program. We've only got a couple hours at best."

Sam had already made for the secret entrance of the hidden lab, but he stilled at the steel in Alan's gaze as the older man watched after him, the uncompromising nature of that look sending chills down his spine.

"You're going back to the Grid."


	2. Chapter 2

**Notes for the Chapter:**

> Fair warning: I am not a programmer. I have no knowledge of coding. I never did all too good any of my science subjects. Anything related is pure magic handwaving and artistic license.
> 
> I managed some math if only to not lose track of shit.

As Sam walked down into the darkened depths of the arcade's basement, Alan's definitive statement echoed in his head ( _"You're going back to the Grid.")_ repeatedly, even though the older man kept the defining features of that plan to himself, ushering Sam down to the lab to get started on his programming. Sam had kept quiet on the lack of details, if only because Alan was right and they were running out of time, and the time dilation equation was going to take a couple of hours, at minimum.

_("You're going back to the Grid.")_

He had to trust Alan, and he did, but something in the way he'd said those few words made Sam incredibly uneasy.

_("You're going back to the Grid.")_

He let himself into the small room containing the laser and his dad's advanced computer sat quietly and powered down, waiting for him, just like he'd left it. A scrap of moonlight filtered in through the tiny window situated above the computer terminal, so he set about covering it up, using an ancient blanket folded double from off the old and sagging sofa in the corner and an equally ancient roll of duct tape, sealing off the small window and cutting off the dim light from the outside.

Once that was done to his satisfaction, Sam flipped on the light switch by the door and powered on the large terminal, waiting patiently as the monstrosity of a computer booted through its start up processes, cleaning the sleek surface of the machine free from dust and grime.

_("You're going back to the Grid.")_

As he waited patiently, Sam crossed the room to inspect the old laser, and remembering from both his father's stories as a kid and his own experiences with the tetchy thing, he quickly unplugged the machine so as to keep it from activating before he was ready for it. It wouldn't do to drop into the Grid before he was finished with his programming and modifying of the Grid's source code.

Satisfied that there wouldn't be any hidden or untimely surprises, Sam took his seat at his dad's terminal and started by opening up a few command windows and got to work in the directories, to start, plugging in his specialized USB drive that contained all the data he'd been tinkering with that was related to the Grid and his private Encom projects. Soon, a dozen different were open, some with scrolling code working in time with his modifications, the work almost intuitive.

Hopefully, he could stop repeating Alan's words in his head, and focus on his tasks.

_("You're going back to the Grid.")_

Before, when he'd just been poking around and looking for curiosity's sake, Sam hadn't actually tried to hack his way through the system, but now, with everything that was at stake for both him and Alan, he concentrated his efforts and utilized every skill he'd ever gained through hacking and his programming classes and whatever he'd picked up on over the years, quickly losing himself to the programming, mind racing with different equations as he simultaneously looked for the source code that would allow him to alter time inside the Grid and wrote a program that would enable a type of quantum entanglement based communications relay that would for real-time comms from the outside.

Focused on his work, Sam didn't really notice as the hours started to crawl by, fingers working furiously across the touch screen keyboard as he processed equations and wrote new algorithms, working out the logistics of the math and the physics in his head, theories and calculations formed and discarded and reworked almost as faster than he could type in the input commands.

Once he was satisfied with the entanglement program, he set it and a few corresponding algorithms to work on manipulating the processing speed of the Grid, slowing it down while writing hundreds of lines of new code to maintain the computer terminal itself. Another part of his dad's genius was that the hardware that contained the Grid was almost entirely self sufficient. Technology had come a long way since Kevin Flynn had first built this machine, and so Sam was now able to tweak the pieces necessary to push it into complete self sufficiency; any and all energy produced by the program running the Grid and the terminal was immediately rerouted back into the system, and there was only a fraction of a percentage lost in the transfer, like 0.002%.

It was all he could manage for now, at least until technology advanced in another leap.

With that goal accomplished, Sam took a look through the code and data of the Grid itself, curious as to what damage had been left behind after the reintegration event, and he wasn't surprised to see that the Grid had been left largely corrupted, but there hope that he could fix a lot of the damage left behind. He started first on infrastructure damages, scraping whole sections where repairs couldn't be made or were compromising other systems, and rewriting and building from scratch what he could.

From there, he moved on to the myriad of individual programs, many of which had been assimilated into CLU's private army. He scrapped what he could of the older assimilated programs, since they were too corrupted to be restored, but there were dozens and dozens of programs that were salvageable, so he set about saving as many as he could.

There were too many for Sam to take care of on his own, especially with his limited timeframe, but he figured he could do some of the rewriting and restoring while inside the Grid, but to help speed up the process, he wrote a new diagnostic algorithm to parse out the corrupted data, although he didn't activate it; it would be of more use on the inside.

He pulled up a digital map of the Grid, only sparing a little surprise as it brought up a rudimentary holographic display, and took only a few seconds to identify from the Grid version of the arcade was situated. It was the moment of a second to start building a new portal in the simulated building, to ensure that 1) he wouldn't have to look high and low for the new portal in order to get out in the organic world again, and 2) keeping the portal close to where he started would only be to his advantage, especially if he got started on upgrading the surrounding area immediately upon arrival.

Eventually, Sam leaned back in his chair, stretching his stiff arms above his head and feeling relief as his spine gave a satisfying series of cracks as he worked to loosen up the muscles in his shoulders. No matter how much he stayed in shape, sitting for hours hunched over a computer screen was hard on the body. He took a few moments to go over his work, scanning through the different screens of scrolling code he had up, checking for any possible errors he would need to fix before activating the laser.

Ultimately, Sam left it as is, satisfied with what he'd accomplished with what little time he'd had and left the lab in search of Alan. He was very curious as to what his pseudo father had done with his time, and as he left the basement behind him, Sam was surprised to see that the arcade was near unrecognisable; a bunch of the old derelict machine lined the boarded up windows, and several had been taken apart and lay in pieces around the arcade. Wires and circuit boards were everywhere, and Sam was forced to watch his step lest he stumble amongst the debris. Alan was nowhere in sight, but he'd obviously been busy as Sam eyed with some suspicion a series of makeshift devices attached to a couple walls in strategic places as his unease from earlier grew in the pit of his stomach.

A peek into the kitchen revealed not the man he was looking for, but he was able to see that the back door leading into the alley behind the arcade was sealed off, and a couple more of those weird devices were in place by the door; no one would be storming the arcade from the back of the building, seeing as there was also a tripwire strung across the sealed doorway.

Whatever Alan was planning (he refused to think too deeply into Alan's unmentioned plan, he wasn't ready yet to face that reality), Sam was getting increasingly worried about the odds of the both of them getting out of this alive. Sam crept his way through the back of the arcade to the stairs leading to his dad's old business office, where a faint light poured out into the narrow stairwell, and it reminded him of his dad's old stories of living here before his revolutionary rise at Encom.

His sense of dread rose as he crept up the stairs, and Sam couldn't help but feel like they were setting up for one final push, a final showdown.

"Alan? You up there?"

"Yeah, in here, Sam." He frowned as he registered just how tired Alan sounded, although he knew the older man would deny it if the subject was brought up. He pushed open the half closed office door to reveal a mess of machine and computer parts, more wires and tubing than he thought possible even with all the spliced consoles in the main area of the arcade. Scattered amongst the mess were bottles of fluid he recognized as industrial cleaners and a few things from the kitchen, too.

Sam was struck with the hope that the basement was reinforced.

"Alan, what are you doing? And where'd you find that gun?"

The other man, standing in the middle of the chaos with a goddamn military issued shotgun strapped to his back, looked up at him from behind a table in the middle of the small space, a wry grin in place. "Gun was your father's; burglary deterrent. Just finishing up these last few bombs; I've got a couple more places for them."

"The hell d'we need bombs for, Alan?!"

Alan's little grin grew at the sound of Sam's alarm and surprise, even as he finished working on his explosive, snipping a stray piece of wire and closing the back of the makeshift casing. "It's just a contingency plan; insurance, if you will. Besides, these and the others are small ones with just enough explosive power to level this building and the next two closest to us."

"...I'll take your word for it." Sam sidestepped a couple pieces of debris and wire as he sidled closer to Alan's workspace. "Anyway, I just wanted to let you know that I've done all I currently can; the entanglement program's up and running and recalibrations are set. For every thirty minutes on the inside, a day passes out here, which means I'll have at least a week on the inside before I have to start to really worry about being trapped, because if you haven't dropped me a line in about a year and a half... then I know that something's gotten really fucked."

Alan huffed a humorless laugh at Sam's words, but he didn't deny them. "Yeah, that's one way to put it, kid."

"And... We need to talk about how you're sending me in alone. This feels too much like a last stand, to be honest."

While the look on Alan's face didn't change, the feel of his expression turned sombre as his gaze was left soft, sorrowful. "That's because it just might be, Sam."

"Can you tell me why?" Sam hated how his voice was so soft and weak, and how his eyes started to blur with tears that he quickly blinked away.

Alan moved away from his appropriated workspace, reaching to gently grab onto Sam with his hands on his shoulders. "Sam... The world's not ready for you, and all that you can bring. It's not ready for the miracles you can bring out of the Grid, either. People are selfish and cruel, and only out for themselves, and I don't think that will change in either of our lifetimes, not if you stay here. So what I'm going to do is ensure that you survive long enough to do something truly special. You deserve to have all your dreams come true, and i know that you'll be able to do something really great, and I only wish that I could be there with you when it happens."

Sam started crying, unable to hold back the tears. "Alan, I- I don't want to lose you too," He hung his head down, tears dripping down his face to land onto the gross dusty floor. Then there were arms wrapped around him as Alan pulled him into a tight hug and Sam returned the embrace, clinging hard to his surrogate father, the only man who'd bothered to care all these after his father vanished, the only one who'd ever cared enough about him.

"It'll be ok, Sam. I promise."

They stood there in his dad's old office, wrapped in each other's arms, unwilling to let go. Alan Bradley had been his father in almost every sense but blood, keeping an eye on him and taking care of him after Kevin Flynn had disappeared twenty years ago, leaving behind a trail of broken promises and broken-hearted little boy, and now they stood at the precipice of losing that connection, and if Sam lost Alan's support, he wasn't sure what he was going to do with himself.

Sniffling a bit, Sam composed himself, pulling back from Alan wipe away the tears from his eyes, keeping his head down as he stifled his own insecurities and fears, because holy shit, it was hard to deal with all of this emotional crap. He glanced up at the older man and tried to smile as he moved for the stairs.

"Come on," He said, his voice a little shaky still, but he ignored it. "I want you to look over my calculations, see if there's anything I might have missed."

"Might have missed?" Alan teased as he followed after Sam, eyes still soft and misty. "I'm sure there's a lot I still need to teach you; then you'll get to see how a real programmer works."

"Ouch, man! Straight through the heart!"

Alan only laughed at his dramatics.

Back down in his father's secret lab, Sam showed Alan the holographic map of the Grid, showing him what he'd done to repair what he could and from there, pulled up the various screens he'd been working with, detailing the algorithms of his entanglement project, and in general, pointed out all the different adjustments and repairs he'd made to the source code. Alan gave some pointers and small bits of advice as Sam gave him the virtual tour, but he didn't really have much to say against Sam's work. He did mention maintaining some kind of virtual armory in the off chance that he would need to protect the portal from any possible hostile encounters, which Sam eagerly agreed to, fingers flying across the keyboard as he implemented the small structural changes with ease.

It was about twenty minutes later when Alan did a double take at one of the command screens, shifting Sam out of the way as he stared at a section of code slowly scrolling the small screen.

"I know this code," he said in a quiet, stunned tone. He pointed to the screen, and Sam could see what was different; this specific code was older than most of his father's stuff in the Grid, and it had different signatures, too. "Can you pull up the program this belongs to?"

"Yeah, sure," Sam agreed easily enough. "It'll just take a sec."

He froze, stunned, and stared at the program name clearly displayed on the terminal screen, dismayed at the damaged and corrupted code.

Alan had found Tron.

"Sam, please move." He eagerly relinquished control of the terminal, moving to stand so that Alan could take his seat, and the older man didn't hesitate as he started working furiously, pulling the original program file to an isolated diagnostics and repair screen with a long practised speed, tracking the corrupted data that Sam knew came from CLU's assimilation and hard reprogramming, but it didn't deter Alan from reformatting whole sections of the corruption, rewriting some the original code from scratch as he repaired what he could manage with erasing Tron's memory files.

"You told me about the corruption, of how CLU played his hand at being a User and the level of his reprogramming, but I didn't think it would be this bad. CLU, for being a copy of Kevin, was not designed for this level of reprogramming, and it shows in how badly he managed to fuck up my security program." Alan was pissed at what had been done to Tron, and Sam got it; Tron was his project, his baby, all those years ago. It was a big deal. "I can't repair everything, not from here, and not without losing everything he is now, but maybe you could help him from the inside, if you find him."

Sam nodded, knowing that this was important to Alan, thinking that if things did wrong, Tron would be his last link to Alan, so of course he was going to help if he could. "Yeah, of course."

"Thank you," Alan nodded gratefully. "I can't get rid of all the Rinzler code, some of it is too well ingrained into his core processes."

They closed down all the different screens and returned everything back to how they found it, plugging the laser back in and Sam left only the laser activation command up on the terminal, ready and waiting for him. It was then, as dawn was quickly approaching to bring about yet another new day, that Sam realized that he and Alan couldn't put it off any further.

What was coming really, fucking terrified him.

Alan sensed his hesitation and dragged him back up into the main floor of the old arcade, with instructions to carefully grab the remaining bombs in his father's office while Alan went to scope out their surroundings through a gap in the boarded up windows.

Sam came back with the handful of bombs and Alan quickly set to work hooking them up in a few locations, one went by the front door, where two more were situated; another was installed in a corner of the ceiling, with the intent of bringing down the roof if necessary; and a couple more were placed amongst the remnants of the old game machines, intent of turning them into shrapnel. The way Alan had it all rigged was if, and likely when, Alan detonated the bombs, the resulting explosion would collapse the building and the surrounding buildings too, collapsing the basement stair but leaving the reinforced basement lab intact behind its reinforced door.

Score another point for Flynn paranoia.

But now, there was nothing left but to send Sam back inside the Grid.

And they were out of time.

"It's time, kiddo," Alan said as he stood outside of the lab. "One of those military humvees was just down the road, and reinforcements should be on their way. We've got minutes, at most."

He pulled Sam into a bone crushing hug, arms wrapped tight around the bright young man he'd practically raised as his own, tears gathering as he felt Sam's arms wrapped tight around his waist, clinging to him like a child.

"You survive, you hear me? Whatever happens, here or in there, I want you to keep going, because you are so special, Sam, and you are going to change the world." He whispered fiercely, choking on the words as he forced them past his tongue.

Sam's breath hitched as he tried to draw in air to respond to Alan, but he failed at that, letting out a choked sob as he cried into his mentor's shoulder, his throat threatening to close as tears slid fresh down his face, soaking into the collar of Alan's button up.

"I- I hear ya. I promise."

"You go through that door, and you don't hesitate. You do not long back, and keep walking strong."

"I promise."

"I love you, Sam. You are my son in all but blood. I love you, and I am so proud of you."

Sam cried harder in Alan's hold, his body quaking from both emotion and exhaustion. "I love you too, Alan."

Alan only held him for a few seconds more before pulling away and giving Sam just a hint of a gentle push for the lab door, a sad, agonized smile fixed firmly in place as he wiped away the tears from Sam's cheek. "Goodbye, Sam Flynn."

Sam nodded shakily, taking a few steps backwards from his surrogate father. "Goodbye, Alan Bradley."

No, that wasn't quite right. "Goodbye, Alan_1."

Alan smirked more warmly at that. "Take care of Tron for me."

Sam nodded again and turned away from the older man, closing the door to the lab shut behind him, locking himself inside. He would not look back, he couldn't.

He had to do this, for Alan's sake.

* * *

With a heavy, world weary sigh, Alan bolted shut the door on his side with a small length of heavy chain and a heavy duty padlock, pocketing the keys before returning to the main floor of the arcade to grab the detonators he'd fashioned earlier from the office, and bringing about the shotgun into a ready position. He'd been surprised that the weapon was still usable after twenty years, but he remembered the old stories Kevin used to tell about fending off potential robberies from back in the day, and Kevin had always kept his equipment in keen working order. Another last look around revealed an old (and loaded) pistol in an old filing cabinet.

Finished with that Alan returned to the main floor to lie in wait for the mercenaries hunting them. Turns out he didn't have to wait long, as he caught sight of the front door slowing easing open, and if Alan hadn't been watching for it, he'd have missed it. Instead, he tucked himself in closer to the old machine he was hiding behind, levelling the shotgun in readiness and sliding the barrel between two of the taller games to give himself some semblance of cover, from both his bombs and the mercs.

He waited until the first bomb detonated, triggered by a tripwire across the threshold of the front door, not waiting for the smoke to clear as the exploded game console rained shrapnel into the squadron of heavily armed men, seeking out all the little nooks and crannies not protected by combat gear, his precise aim allowing him to take out one merc with a blast to the face. He fired again and again, taking out another two before they got a bead on his location and he was forced to abandon his position, bolting for the Tron game in the corner, swinging his rifle around to bash a third merc's head in.

He detonated another series of bombs, sealing the mercs inside the arcade with him and cutting them off from their reinforcements, ducking as they fired on him, a couple of bullets slamming into him and sending him crashing into the game.

Alan dropped the empty shotgun and pulled free his pistol, shooting another merc in the face before ducking into the basement stairwell and closed the Tron game behind him, even as a few more bullet tore through his right side, blurring his vision with white-hot pain as blood dripped copiously down his flank, and even breathing hurt at this point.

Already dizzy from the blood loss, Alan was keenly aware that he only had minutes left, so once the basement stairwell was sealed, he dragged himself down, nearly falling down on his face. The stairwell was sealed on this side of the door, giving him just enough time to stagger his way to the lab doors and leaving a large trail of blood behind him, where Sam should already be gone, and he collapsed against the padlocked doors as his lifeblood leaked slowly from his body. He had very little time, he couldn't fail Sam now.

Vaguely, Alan could hear yelling from the main floor, but he paid it no mind, dropping his pistol to the concrete floor, scrambling for the detonator for the majority of the bombs left that would seal this place off from the outside. He had to use both of his shaking hands to push down the button, but he grinned weakly as the bombs worked as planned, collapsing the stairs into the basement, but where he sat propped against the wall, only dust trickled down from the ceiling.

Alan didn't really mind that this place would become his tomb.

Sam was safe, and he would stay safe, and that was what was important.

One day, someone would find again like Sam had done with Kevin two years previous, Alan knew that, but it would hopefully be years from now, and maybe then, the world would be ready for Sam and the change he and his Grid would bring.

He was tired, now, and he was starting to feel a little cold.

His breathing was growing shallower, and he could no longer feel anything below the waist.

At least his gunshot wounds didn't hurt anymore.

Sam was safe, so maybe he could rest now.

Alan smile as his eyes drifted shut.

So tired, but that was ok.

_Kevin, you would be so proud of your son._


	3. Chapter 3

**Notes for the Chapter:**

> This chapter is the start of the real major changes of this rewrite. Format might be a little off, as I'm doing this from my phone. If there are errors, I'll fix them ASAP.

Leaving Alan behind, knowing that it was likely the last time he would ever see him again, was probably one of the hardest things that Sam had done in his life. It was unbelievably difficult to not look back as he walked through the door into the basement lab and closed the door behind him, but he'd promised Alan he wouldn't, and he'd be damned if he broke his word now.

He faltered only once, leaning heavily against the closed and locked door, his forehead bowed against the heavy wood as he listened to Alan's footsteps creep away, and he flinched at the uncompromising sound of padlock used to seal him in. His fingers itched to try and throw open the door and run after the man who'd taught him everything he knew, who had taken the time to give a damn about him when no one else had ever bothered after his dad had disappeared.

With a heavy heart, Sam sighed and moved away from the door. He needed to focus on the task at hand, even though he was absolutely terrified, and they were out of time. The way he had it figured, he had about a week, give or take a couple of hours, before he could legitimately start worrying that things were fucked on this side of the digital world, but the point of no return for Sam was if two or three months passed with no word. By the end of three months of Sam being inside the Grid, almost twenty years would have passed, and Alan was likely to have died.

What Sam had told Alan was true; if Alan couldn't get word to Sam in at least a year, then things were still fucked and Alan was likely dead or in prison.

Sam realized, somewhere deep in his soul, that he was likely relying on a random stranger stumbling upon the computer terminal for his release back into the organic world. He really would have preferred not leaving that to chance, but it wasn't exactly like he had a choice in the matter.

He just hoped the world would be in a better place.

Still, he couldn't hesitate; he could not look back at what he was leaving behind. Sam had to stand tall and face his future inside the Grid, and he would survive and thrive, and he would change the world, if only for Alan's sake.

He had no idea how he was going to make that happen, but he had time to figure it out.

Sam sat down in the old chair at the terminal, where behind him sat the primed and ready laser that would digitalize him into data to send in the Grid. He ignored how uncomfortable the damn thing made him and just stared for a moment at the activation screen.

An explosion from upstairs jolted Sam from his melancholy and he raised panicked eyes to the ceiling above him as a small cloud of dust floated down from the rafters. They were out of time!

Sam slapped his hand down on the 'yes' key, activating the laser and before he could blink a bright flash of light surrounded him and once again, Sam was inside the Grid. Vertigo had him bracing himself on the desk in front of him, even as his eyes adjusted to the dim lighting and darker colors of the Grid, and with a look out of the small window, he could see lightning crackle and flash across the thin strip of digital sky.

Looking down at himself, Sam found himself dressed in the formfitting black jumpsuit and armour (black highlighted with glowing white circuitry) from his first trip into the Grid, and he was instantly relieved by the comforting weight of the identity disk attached to his back.

He took a few minutes to just sit there and breathe, composing himself in order to do what was needed of him; he had a week before he could realistically expect Alan to get a hold of him, so Sam needed a plan on what the fuck he was going to be doing here.

Okay, time to make a list: 1) the Grid was likely damaged from the Reintegration Event, so damages needed to be assessed, especially here in Tron City, and eventually repaired; 2) the building he currently occupied (and eventually the surrounding area) needed to be fortified against any and all hostile threats, be it from programs or bugs; 3) because of the equivalent of a thousand years of CLU's propaganda against Users, he needed to suss out and find allies, because there was no way he could do this alone (even his father had Quorra); and 4) he needed to figure out what he was gonna do about Tron.

In terms of priorities, Sam knew that number two on his list was the most immediate, followed by some variant of number three. Number one was the big ticket and would take the longest and would take the most resources (once he had them).

With the most basic of plans in mind, Sam pushed away from the desk to check out the rest of the building. The digital version of his father's secret lab was much larger than the last time he was here, with an enclosed portal occupying most of the expansion, looking very much like a teleportation pad from those old sci-fi shows he watched as a kid. Looking back at the desk revealed what looked like a sleek PC set up, with a touch screen keyboard and an elegantly curved monitor and a few touches to the keyboard showed Sam that this was his method of communication with the outside, using the real-time quantum entanglement comms program he'd developed.

Leaving his new comms room, Sam was a little surprised to find a veritable armory, like straight out of a futuristic spy movie with an array of laser rifles racked against the entire north wall, glowing white tables and shelves lined with pieces of equipment. Each table and shelf was labeled, thankfully, as Sam couldn't parse out the different pieces in their inactive forms. A row of lockers revealed a bunch of harnesses, so Sam started there, strapping a harness across his chest and waist which molded perfectly to his armour. He then clipped what was supposed to be an energy shield to his left wrist, a collapsed laser rifle to the small of his back, and the baton of an energy sword to his hip. The sword especially reminded him of lightsabers, which made his inner child gleefully, ecstatically happy, and yeah, he was that big of a nerd.

Each of the weapons synced up with his Identity Disk, giving Sam the innate knowledge on how to use these weapons, which he supposed was a perk of the digital world he was in.

Sufficiently armed, Sam left his armory to case out the rest of the building, ultimately finding it just as bare of furnishings and purpose as his first visit, and the streets visible from the windows were chillingly empty, although even so far away from where the original portal had exploded, he could see of the damage caused by the system wide explosion.

Some of the tall buildings nearby were derezzing slowly, dissolving pixel by pixel, and it looked like there were section wide blackouts too. The digital skies were just as turbulent as before, lightning flashing across the blackened sky in complicated circuit patterns, although even from street level, Sam could see the light trails from light jets, and even a couple of Recognizers.

It looked a lot like an aerial dogfight, which meant no going outside until he was sure he could keep himself safe and alive. But he needed information on the state of the Grid and the rest of Tron City, and that meant he needed to find a program he could trust, and that meant leaving the relative sanctity of the virtual arcade.

Or maybe...

Sam was a User, one that already extensively modified the source code of the system. His father, Kevin Flynn, was the first User to come down here, and as The User, the Creator of this system, he'd been able to manipulate the environment of the Grid as easy as breathing, creating new programs and porting over old ones, writing new functions and new system commands effortlessly while on this side of the computer screen.

What was stopping Sam from doing the same thing?

How was he supposed to do that, though? How was he supposed to harness his abilities as a User?

Maybe all that was stopping him was the limits of his imagination, of which he had in spades. So logically, his first order of business was deciding what he needed the most.

Sam needed someone to watch his back, someone to go where he couldn't. He needed an ally in a world that didn't trust him and would likely kill him first.

Sam needed to create a program of his own, but he needed to learn from his dad's mistakes and not create another CLU.

He retreated from the front of the virtual arcade, back down to the basement to the comms room, heading for the unoccupied wall on the far side. He ran a hand lightly across some of the glowing circuit patterns on the wall, watching as they glowed brighter beneath his fingers. Closing his eyes, it still took a few minutes for his perception to expand beyond the limits of the outer world but now he could almost feel the invisible source code of the building and the digital rock beneath it. He pulled at some of the fragments, opening his eyes as a room opened up before him.

The room was a little on the smaller side, maybe about eight feet across and about as tall, with dark, sleek and glossy walls and only a faint illumination in a dim lit cyan color coming from an intriguing hexagonal pattern on the floor.

Sam dropped lightly to his knees and pressed his fingers to the floor in front of him, using his heightened perception to grasp at the code in the air, and activated the neural interface, which in turn activated an interactive touch sensitive hologram. He got back to his feet as a full sized adult incubation tube rose into existence in front of him, a blank humanoid shell already floating inside, ready for him to build upon.

The first question was what did he need in a program of his own. CLU had been a codified likeness utility, modeled too closely after his father. A utility program was a good start, but he also needed vast amounts of information so a query and search function was a must, and maybe a backup security function for self defense. He also added some administrative permissions and an adaptive operating system. Add in an advanced encryption setting to help prevent hacking from hostile functions, even if his program was captured by hostile forces. Anything he could think of to protect and enable his program, he added to the root code of what (who) would be his most trusted ally inside the Grid.

A quick look to the tube had Sam blinking in surprise at the twin likeness of the program inside. "That is so freaky…" he muttered as he returned to the holographic interface, still unnerved to feel the minute amount of pressure beneath his fingers.

Sam decided he didn't want his program to look like a carbon copy of himself, so he dug around and found the equivalent of a character creation screen, which brought a small, grudging smile to his face.

He didn't tweak much, darkened the hair, changed the eye color, broadened the shoulder span just a touch, and he gave the inactive program a couple more inches of height (he'd noticed that most programs were really tall for some reason) before naming him and closing the interface.

He watched as the incubation tube glowed brightly as the program compiled before the liquid inside drained and his program stepped out soundlessly. Sam could only stare as he took in the living, breathing being he _created_ standing before him with a blank, expectant expression gracing pale skin. He was dressed much like any other program he'd seen, entirely in black but the armour was styled a little differently and he also sported a long black coat that fell to mid calf and a visor that curved around the right side of his face to cover one eye. The glowing circuitry patterns boldly bisected the torso and curved down in symmetrical lines and shapes and the color was primarily a teal blue with smaller circuit nodes in yellow.

"Do you know who you are?" Sam asked quietly, near vibrating in anticipation. Creating a program while inside the Grid was a whole different animal, and he wanted to know if he'd done it right.

"Yes. I am Gemini, a systems utility program designed with an adaptive cognitive processor, and several enhanced admin and security functions. How may I serve you, SamFlynn?"

The voice was a little flat, but hopefully Gemini's adaptive cognition would allow the program to develop a bit more of a personality over time. The baby program just needed a little experience in the world in order to learn.

"Just call me Sam," he said as he left the small room with Gemini following a step behind him. "For now, I'll need some help in fortifying this place. You should have the necessary permissions already enabled."

Sam stayed in the basement in order to mess around with the base infrastructure of the building and surrounding streets while Gemini went upstairs to make his own modifications. Again reaching out with his enhanced perception, which he was finding to do as time went on, Sam strengthened the foundation of the building and was able to enable a type of proximity alert surrounding the area about fifty yards around and set it to sound when anything larger than a light cycle came within its borders.

With that done, Sam joined his program upstairs on the main level of the arcade, pleased to see that Gemini had already made the windows smaller and tinted them and was already creating a small room close to the entrance of the arcade. Sam didn't know what it was for yet, but they had time. It was the matter of twenty minutes to build some basic furnishings; a bar and some stools towards the back by the basement stairs, a couple of comfortable chairs, a large table near the tinted windows that Sam was going to install a map of the Grid to, and even built a couch. It made the space much less empty, but there was still room to add whatever they were going to need as they needed it.

Leaving Gemini to continue with whatever modifications he wanted to add, Sam made his way up the narrow set of stairs to the office overlooking the arcade, sighing as he stretched out tired limbs. Exhaustion was starting to creep in, settling in his bones and making his hands twitch. He had a serious headache building at the base of his skull and behind his left eye. There wasnt even any coffee to push back the symptoms, so Sam was left to suffer for the time being.

He was reaching his limit, though, after being awake for approximately two days, and he could feel the effects of his adrenaline fueled run start to fade.

Looking around him, Sam decided that this space was going to be his home, his place to relax and sleep, so he set about crafting himself a bed. He also added a couch to one wall and a small table and a lamp that emitted a soft white light. He added shutters to the window overlooking the arcade and had to turn away from the now-tempting bed; he still had a few things to do before crashing.

"Gemini, once you're done with what you're currently doing, would you mind setting an alert to the comms for any incoming transmissions?" Sam said as he came back down to the main level, smiling as the program nodded. "After that, I'd like you to scout around the neighboring sectors and get a feel of the system. Arm yourself appropriately and try to blend in as much as possible. No one can know that there's a User in the system."

"Of course, SamFlynn. I shall proceed with due caution." Gemini said blandly as he finished his current task and moved around Sam to get to the basement.

"Come on, I told you to just call me Sam."

"You will likely be required to tell me again." Came the surprisingly sassy reply that echoed off the walls and it startled a laugh from Sam.

Guess Gemini had no problem adapting a little personality already.

A low rumbling purr, dangerous and _familiar_ echoed behind Sam and he stiffened in fear as the sound sent icy chills down his spine.

Sam knew that sound, that deadly, dangerous ticking growl and he felt the phantom hum of a disk at his throat, remembered being pinned so effortlessly by the weight of a body on top of his and he forced himself to turn around ever so slowly, knowing instinctively that too fast was a swift death.

His hand creeped up behind him, reaching for his identity disk on the off chance he could defend himself, but the sight of Rinzler slumped against the open doorway of the arcade had Sam hesitating.

CLU's enforcer, dark and deadly and gracefully relentless, slid a few inches down the side of the door, his limbs failing to keep him upright. His armour, once impeccably sleek and shiny, was now scuffed and battered, marred with scars and scrapes, and one arm was wrapped around his torso, drawing Sam's attention to a horrific injury with slowly derezzing code splintering away into nothing like embers in the wind. His bright red circuitry kept flickering from that dangerous red glow to a blue that Sam recognized from stories told to him as a kid, highlighting the small glowing panels at his throat that formed a very iconic T shape. His face was hidden behind the shiny opaque helmet, blocking a familiar face from Sam's horrified view.

"...User."

Sam had long ago figured out that Rinzler was the rectified version of Tron, corrupted and repurposed by CLU for reasons Sam couldn't fathom, and it broke his heart to realize that for close to a thousand years his father had never realized his friend was still alive - of a kind.

Still didn't make him any less dangerous as Rinzler, but Sam had promised Alan that he would try and save Tron, and he wasn't going to waste the opportunity.

"Who are you? Rinzler or Tron?" As much as Sam would like to help Tron, he needed to know the answer to that question first.

The low growl hadn't ceased, but Sam was starting to think it was subconscious at this point or maybe a sign of CLU's corruption, and he waited breathlessly as the silence hung between them, one hand now firmly grasping his disk, just in case. He was also vaguely aware of Gemini's presence at the top of the basement stairs behind him, disk out and keeping still, waiting for Sam's lead.

"...User… fight…" Rinzler slurred as he took a fumbling step into the arcade and closer to Sam, and he nearly fell to his knees with the effort. "...fight… for the Users." Another staggering step forward. " _Whoami_?... I, I am… Tron."

Tron's strength failed and Sam lunged as the damaged program fell forward in a dead faint, Gemini at his side to take some of the weight. "Upstairs, we'll take him upstairs and then you'll seal that door with a passcode."

Between the two of them, they managed to drag Tron up to Sam's room and gently deposited him onto the bed, Gemini hanging around for only a moment longer than necessary before darting back down to complete his given task, leaving Sam alone with a broken Tron.

Sam very carefully turned Tron onto his side to gain access to disk on his back, unlatching it and with a few rhythmic taps to the unlit edges of the dual disk, he was able to bring up Tron's root code, the holographic interface rendering in a simplistic yet complicated helix pattern that looked a lot like Quorra's DNA structure.

The realization hit Sam like a semi even as he looked through Tron's code: the ISOs had spontaneously evolved out from the Sea of Simulation, and the last he had seen Rinzler had been as he fell into that very same Sea. It stood to reason that the Sea had altered Tron in some fashion, and it also alluded that the Sea was recovering from being poisoned by CLU.

Shaking his head to get back on track, Sam studied the code in front of him, somewhat aware that Tron's functions had been suspended, halting the derezz in its tracks; good, that would give him time to work. Sourcing out the damage, Sam saw the obvious one in Tron's side, but there was also something wrong with his left leg and a crack in the helmet hinted at some damage to his face and head. The rest of the damage was attributed to the corruption, which glared an angry red. Remembering how his father had regenerated Quorra's lost arm, Sam tried to do the same thing here, isolating and deleting whole sections of corrupted and damaged code, rewriting lines and lines to fill in the blank spaces, and once he had enough fixed, he also activated the program's self maintenance functions and firewalls, which went a long way to helping contain the corrupted code.

It kind of pissed Sam off to discover Tron's firewalls had been disabled by CLU, likely to smooth the way for rectification.

By the time he was finished, there were only a few small pockets of corrupted data that he couldn't fix, the damage too enmeshed into vital functions, and Sam's vision was swimming, but he could tell that what corruption remained was contained and couldn't do any more harm. Tron was just going to have to come to terms with the remnant echoes of being Rinzler, and Sam would be there for him if he could.

With shaking hands, Sam reattached the disk to the port on Tron's back, pleased as the disk locked into place with a final click and the stasis enabled, allowing the reworked code to compile and manifest in a gentle light show glowing a soft green.

That was a new color; must be the repair matrix.

With a tremulous sigh, Sam swayed where he stood, and he quickly sat down on the floor, lest he fall over. His eyes drifted shut without conscious thought as his exhausted body screamed at him for reprieve. He leaned back against the side of the bed, near hypnotized by the soft hum echoing from within Tron's helmet.

He dozed for a few minutes until Gemini touched his shoulder, staring at him with a concerned frown. "SamFlynn, you are in need of rest."

"Can't argue there," Sam said with a tired grin.

"Sleep. You will be safe here while I complete my mission. I should be back shortly."

"Please be careful, I can't lose you, Gemini."

His program nodded briskly before leaving the room, disappearing without a glance back and Sam allowed himself to drift off back to sleep, oddly comforted by the low hum above him as Tron regenerated and healed.

* * *

Sam came awake with a gasp, frantically panting for air, disoriented as visions of pain and death and fear flashed through his head, the remnants of his dreams (nightmares) spinning behind his eyes as the tears started to flow and his gasping breath turned into choking sobs.

Sam wrapped his arms around his knees, hugging himself tight as Quorra's bright inquisitive smile turned to dead unseeing eyes and blood. Alan standing in front of the board of directors with an energetic smile that made his look years younger turned to a tired older man, clothes dirty and worn, resigned in his impending death. His mom's beautiful face slowly vanishing from his memory, an old hurt brought back to the fore by recent events. His dad's heartbroken look as he recounted failing Tron all those years ago, shifting into the arrogant cruelty of CLU's sense of superiority. His little rescue, Marvin, playing at his feet with his favorite toy, just another innocent victim as his house by the water burned with vindictive rage.

He sobbed through his grief, his cries echoing off the walls, and he became vaguely aware of another presence, of comforting arms holding him close to a warm and solid chest, of his head tucked under someone's chin and he turned into the embrace, wrapping his arms around the other in a desperate bid for stability even as his body shook with grief and tears poured relentless down his face.

He cried for the loss of his envisioned future, of bringing his father's miracles to the world he cried for his helplessness and the futility of running from those trying to kill him; and he cried at the sad and twisted irony that he was in exactly the same position as his father twenty years ago, likely trapped inside the Grid with no way to get out, because realistically Alan was dead, and so he cried at the loss of the last of his family.

Eventually, the tears slowed and Sam was able to breathe properly, but he wasn't ready to face the world yet, so he kept his face turned into the body holding him, safe and secure as he recalled Alan's words to him _("You survive, you hear me? Whatever happens, here or in there, I want you to keep going…")_ and he allowed those words to bolster his flagging spirit.

With his body trembling and a shaky sigh, Sam pulled away slowly and raised his head to look at whoever had held him in his grief, but he froze in surprise as he took in the subtle worry on Tron's _(Alan's)_ face and the dark hair and the curiously gray eyes that were watching him with a hint of trepidation but the security program looked whole again save for angry scar running down from the corner of his right eye to his chin.

"Tron…"

"Are you alright, Sam?" Even his voice was the same as Alan's, sure and confident but different in a way that made Sam's senses take notice.

"No," he replied with a sad, rueful smile. "But I will be, someday."

Tron watched him for a few moments, trying to determine if Sam was lying, but he seemed satisfied with Sam's answer as he got off the bed, offering Sam a hand up.

Sam took it gratefully, although he was confused a little, as the last thing he remembered was falling asleep on the floor, and he also wondered how long he'd managed to sleep for.

"How long was I out for? And uh, how…" he trailed off, feeling heat creep onto his face as Tron regarded him with a hint of amusement.

"You were still passed out after I came back online, but you didn't seem all that comfortable, so I moved you." The tiniest flash of a grin quirked up as Sam groaned with embarrassment. "As for how long, it's been 5.2 hours since you repaired me."

"Well, at least I got some sleep," Sam said as Tron led them downstairs. "What have you been up to since I was out? And where's Gemini?"

"Your program's currently out on recon, scouting around a few sectors for information. He's very smart, you did a good job with him," Tron's words made Sam's chest tighten with a feeling of pride and he ducked his head away from Tron's intense gaze. "He showed up after I came back online and showed me around. You two have done some good work. I stayed behind to keep you safe, since you were currently unable to defend yourself."

"Does that mean you're gonna stick around?"

Tron nodded briskly. "Yes. My purpose is for the Users, to protect the system for you. You gave me that purpose back."

Sam shrugged off the sentiment, mildly uncomfortable in the face of Tron's gratitude. "It was the least I could do besides, Alan asked me to help you, if I could."

"Alan-1? My User?"

"Yeah, he's the one who sent me down here, and he was able to repair some of your code too." Sam sighed again, not wanting to think of Alan likely being dead. "Look, a lot has happened, and we've still got a lot of work to do. Are you gonna be ok?"

Tron was quiet as he contemplated Sam's question, features carefully void of any emotion. "I… I will be. Regardless of my User's request, you did not have to save me, nor were you expected to, especially after my actions as Rinzler. For that, you have my everlasting gratitude."

Sam waved him off with a tired smile. "It's ok, you know. I would've done it anyway. If it helps, I forgive you. Now, what can you tell me?"

Tron walked him to the large table he'd built earlier, where an intricately detailed holographic map of the city was sectioned off in color coded sections that Sam couldn't make sense of. "These sections in white are currently unknown status, while these here and here in red are actively hostile either against Users or just the rest of the system, while these few in yellow are neutral."

"And the lone blue sector?"

"That's us."

"...Oh."

Sam spied a single blue bit touring through the streets of the one of the farthest yellow sectors and he pointed to it, expanding that section of the holloman. "And what's this here?"

"That's your program, Gemini. He's just scouting for an outline of the city, and I've cautioned him to run at the first sign of trouble." Tron pointed to a few of the neighboring sectors in white, which dominated the board by more than half. "We may have some problems with hostile gangs later on, but for now, the city will be trying to fill the power vacuum left by CLU, and since the Reintegration, the city's under swarm from gridbugs from the outlands."

Sam grimaced, absolutely disgusted. "Gridbugs?"

"Disgusting things that eat away at the system code, leaving nothing behind. That's what these few null sectors on the outskirts are; dead sectors. Fortunately for us, gridbugs work slowly and can be driven off entirely." Tron identified the sectors in question and Sam nodded his understanding of the situation.

"So I've got a lot of work to do, cleaning up my father's messes." The task ahead seemed daunting, too large for his scope, but realistically, Sam had nothing but time. He would manage, he could make do with what he had. "The portal closed while I was passed out, I'm assuming?"

Tron hesitated for a moment before nodding just once. "Yes, just a millicycle before you woke up. You needed the rest."

Sam nodded, leaning against the console with his shoulders hunched. "Yeah, I probably did. Everything went to hell so fast, all Alan could do was grab me and run."

Tron put a comforting hand to his shoulders, and Sam could feel the heat of him through his suit. "I'm sorry, I wish there was something I could do to help."

"Honestly, I'm just surprised that you're as ok as you are," Sam leaned into Tron's presence, smiling at him. "You've had a lot of trauma happen to you; it would not surprise me if you still had trouble dealing with that shit."

They watched the little blue bit that identified Gemini start to circle back in the direction of their home base before Tron spoke again. "I think… it's different for programs than it is for Users. I remember everything, and I feel… terrible and guilty. But it's safely contained behind a wall in my mind and it can't hurt me or the ones I care about anymore."

"Yeah, that makes a lot of sense." A tremor suddenly wracked through Sam's body as memories of his own trauma ate away at his subconscious, ever present in his mind. Tron's grip on his shoulder tightened then pulled him closer into a comforting hug, and Sam couldn't stop the tears.

He told the security program everything, from the second he left the Grid two years ago, sharing all the adventures with Quorra discovering humanity, to the advances he'd engineered at Encom, turning the company on its head and revolutionizing several fields of science, from biology and biochemistry to medicine and bioengineering to computer sciences and mechanical engineering to advances in space tech and quantum mechanics, and all of it derived from ideas built off his father's old notes and his own designs and from Quorra's brilliant innovations that could only come from something other than human.

As tears slid down his face, Sam spoke of military and government intimidation as they tried to come after his ideas and innovations for weapons manufacturing and advancing the military might that even in the beginning Sam could see would only lead to more and more war that the world did not need. As his voice started to crack and tremble, he spoke of betrayal from within, of how Dilinger turned out to be such a snake for such a gifted mind, accepting military contracts in return for control of his company.

Sam had blocked every move to seize his company until the Government decided to steal it in force by way of a coup, of cornering Quorra in one of the labs and killing her when she refused to comply. He told Tron of how she'd given him precious time to escape with Alan, even destroying as much of their work as she could before her death. He whispered fearfully of how her dead sightless eyes staring at him was a sight that would haunt him for the rest of his life.

Sam slowly gave words to the harrowing run through the streets with Alan, of how adrenaline was the only thing that stopped his paralyzing fear from taking hold, and of how Alan was likely dead but how he still clung to a smidgen of hope, and would for at least a week, explaining the timeline he and Alan had given themselves.

When the words finally stopped, Sam realized that they had migrated over to one of the couches, where Tron was holding him in his arms, like he was trying to protect Sam from the rest of the world.

Sam felt _wrecked_ , drained in a way that spoke of an intense emotional outburst, and all he wanted to do was sleep. Spilling his soul to Tron was a step in the right direction of getting closure, of healing his trauma, but he also knew that there were more breakdowns in his future as he learned to deal with all the wounds to his heart and soul.

If Tron stayed with him, always a hero to him, then maybe Sam could learn to live again.

"Are you feeling better?" Tron asked him in a soft tone he couldn't identify but it made his heart skip a beat.

"For now," Sam gave Tron a humorless grin, wiping away the trails of salt from his face. "Can't promise that won't happen again, though."

"I'll be right there beside you, every step of the way, if you'll have me." It almost seemed like Tron was trying to tell him something, hidden in the subtext, but Sam was too emotionally drained to decipher the program's meaning.

With one smooth motion that stunned Sam, Tron stood from the couch with Sam in his arms, ignoring his protests that he could walk with a look so much like Alan's 'I don't think so' expression that Sam's breathe stuck in his throat for a moment. He carried Sam like he weighed nothing at all, a thrill tingling in his fingertips at the show of easy strength, and Sam could not get Tron to budge.

Tron brought him back upstairs, depositing him onto his bed with a gentle ease. "Get some rest, Sam. You've had a hard day."

Sam couldn't even argue because sleep was already dragging at him with heavy limbs and heavy eyes. "What about you?"

"The first couple of days will be solely dedicated to information gathering, and I can easily coordinate with Gemini on the matter." Tron pulled a blanket over Sam and dimmed the lights to almost nothing. "I'll have a list of tasks ready for you when you wake up."

Sam was already fading into the depths of sleep, barely aware of fingers gently touching his cheek.

"...I'm glad you're here, Tron."

"Me too, Sam."


	4. Chapter 4

Gemini didn’t get back from his recon trip for another five days, and Sam itched from the waiting, growing restless but it gave them a more complete map from which they could work with, and that soothed Sam’s impatience. Gemini did not have as much (or at all) good news about activity within the city.

“There are a few sectors that are Neutral, maintaining a stance that they just want to be left alone from the fighting, but the general consensus is that they won’t stand to be controlled, either,” He said, pointing to the few sectors color coded in yellow. “Sectors Gamma and Iota are especially against the unrest caused by the gangs and CLU’s forces and are more likely to respond in kind to any action taken against those living there.”

“We can use that,” Tron said, tapping the interface to mark the sectors in question. “Not now, but eventually.”

"When Kevin Flynn was first cut off from the portal, and right before the Purge, the city's population stood at over sixteen million: best estimates now are closer to under two million, what with the forced volunteers for the Games and the conflict resolution of any uprisings. Even more were derezzed after the Reintegration Event."

Sam looked over the map, eyeing the red sectors that took up most of the city before pointing to a couple of sectors not lit up on the edge of the city furthest from them. “What are these ones here?”

Gemini looked haunted for a moment, a fact that startled Sam. “Those are… dead sectors. I think there’s maybe ruins left and not much else.”

“What took them out?”

“Swarms of Gridbugs, from the looks of it,” Gemini shrugged a little helplessly. “I didn’t stick around, didn’t want to push my luck, if I’m honest.”

“Good; I want you to stay safe more than anything.” Sam said firmly. “So, what’s our next step?”

“First thing tomorrow, you and I can go out to begin repairs, all you need to do is pick a sector to start in.” Tron manipulated the map to magnify one of the neutral sectors close by. “I’d recommend starting here, in Sector Theta; there’s not as much damage as some of the others and being in a neutral zone, we would be less likely to be accosted by hostiles. It would be good practice for you, as well.”

Sam couldn’t really argue against the security program, his logic was sound. “You’d be coming with me?”

Tron gave him a look that was clearly unimpressed, like Sam knew better and wasn’t an idiot, so please, stop playing dumb. It made Sam feel like he was on the receiving end of one of Alan’s more disappointed lectures. “Of course I am; you’re not going anywhere without me if I can prevent it.”

“Of course. Didn’t mean to imply otherwise.” Sam minimised the map, drawing it closed with a flick of his hand and a touch of power. Gemini grinned at the both of them as he moved towards the bar, ducking around the other side to draw himself a glass of energy before pulling two more glasses from the underside of the counter.

That was something that Sam still wasn’t used to; the concept of pure liquid energy as fuel, instead of food. Food could be processed and created for consumption, like the meal he’d shared with Quorra and his dad that night a long time ago, but it didn’t really do anything, not like in the outside world.

The taste, depending on how it was mixed and served, varied from sour Granny Smith apples or fresh cut pineapples or smooth spiced peach whiskey. Sam sipped at the glass Gemini handed him, relishing in today's whiskey flavor. Sam had also discovered that the brightly glowing energy didn’t provide quite the same thing for Users as it did for programs, but it would sustain him for however long he was going to be stuck here.

He wasn’t exactly optimistic about Alan contacting him in the next day or so; he knew in his heart that Tron’s User was likely dead, and likely had been since he was digitized, if not shortly after those explosions. Still, the Grid and its cities (of which there were a few more beyond TRON City, surprise) were his home now, and he had a purpose here, and he wasn’t alone either.

Gemini was the best thing he’d ever created, and he loved his program much like a parent, feeling incredibly proud the more he watched the utility program learn and evolve, and he was especially fond of the way Tron treated his program, like a protege of sorts. The interactions between the two programs always made Sam smile, and it went a long way to soothing his still-wounded soul. Tron was always patient, teaching Gemini whenever he could or giving advice, and he suspected that Tron appreciated the company just as much as the younger program did.

Sam made his way down to the basement, specifically his little room where he’d created his program. In the couple of days while waiting for Gemini to come back, he’d expanded the space a bit, turning it into a bit of a tinker’s lab. There was now a draft table where he could draw out his designs as well as a filing cabinet that was isolated to its own private and locked server. Since Tron seemed pretty militant on keeping him safe, and therefore inside, Sam whittled away the time down here, trying to see what he could come up with.

His current project was based off of old concepts for scout drones, because Rho Sector may have been one of the smaller sectors in the city, but it was still much too large for one program to effectively patrol, and they could not afford to be taken by surprise by any enterprising or adventurous programs, or by any of the rival gangs.

He wasn’t sure if he wanted his drones to be strictly scouts, or if he wanted to give them some defence capabilities, which he would need to alter the current design for. Currently, they were unobtrusive, designed to give a signal to Tron or Gemini if tripped, but even equipping a small weapon would increase the size, making them easier to spot and be taken down by a sniper unit.

“Your thinking is automatically limited by the constraints of the world you were born in,” Tron’s voice at his ear caused Sam to flinch minutely. He tilted his head to look at the security program crowded up behind him, focusing on how close Tron was. “Kevin always said to think outside the box, but it was more like he was reminding himself of the fact that the Grid can do more than he was used to.”

“What would you recommend, then?” Sam asked in a near whisper, not wanting to break the closeness between them. He could feel acutely the heat from Tron's body, making his own body hyper aware of the proximity and craving something more.

One corner of Tron’s mouth quirked upward into a small amused grin as he reached out to touch and manipulate Sam’s drone design. “The initial design is good, but the physical size shouldn’t matter since the right code inside the shell should allow for replication of the drone’s needs.”

It was crazy how intuitive Tron was, but he was a security firewall, and Sam had no trouble following his intuition or thought patterns. “Replication… like nano-technology. Ok, so I gotta think more science fiction; I can do that.”

“Not right this moment,” Tron minimised Sam's designs to an inactive state and dimmed the light above Sam’s workstation, gently pulling the User to his feet. “You need to be thoroughly rested for our mission to Theta Sector. Time away should give you insight later.”

Sam rolled his eyes in exasperation but he allowed the security program to drag him up to his room without complaint. “You know, I never expected you to be such a worrier over my basic health.”

“You’re a User; keeping you at optimal levels is kind of my priority.”

“Is it _just_ because I’m a User?” Sam asked from his seat on his bed, pulling off the different pieces of his armour, setting them aside in a pile beside the bed; it was much more comfortable to sleep with it off.

“No… no, it’s not just because you are a User.” The softness of Tron’t voice had Sam looking to him where the program was sitting on his couch, hands clasped together with his elbows on his knees, a move that Sam had seen Alan do more than once over the years. “You are important to me, Sam.”

Heat bloomed in Sam’s face at those soft spoken words, and he knew he was blushing. “You’re important to me, too, Tron.”

“Because of my User?”

Sam shook his head, smiling shyly. “No, for more than that. Yeah, you remind me of Alan, and not just because you look like him, but in a lot of ways, he was like my dad. You’re… definitely not.”

“Oh?” There was an amused lilt to his tone and Sam had to laugh, if quietly.

“Oh, yeah. You’re only parental to Gemini. No, I care about _you_ , Tron and not at all like a parent.”

Tron chuckled as he stood from the couch, the sound warm and melodious, curling into the cracks of Sam’s psyche like honey and smoke. The security program crossed the room in unhurried steps, reaching into Sam’s space, leaning over him to unlatch the disk dock from his spine, circuit laced fingertips sending curious trails of fire where he touched.

“Get some rest, Sam.”

Sam shivered at the low rumble in Tron’s voice, at the feeling of his body so close, and he prayed that he wasn’t misinterpreting the signs. “What about you?”

“Me?” Tron was still in his space, his face inches away, his hand still tracing patterns across his back.

“You can stay,” Sam whispered, watching as Tron’s eyes darkened in promise.

“If you’ll have me, Sam.” Sam smiled and scooted backward across the bed, providing enough space for the program to join him, hoping that the invitation was clear enough. Tron smiled back at him, like he was precious before moving away long enough to remove some of his own armour before climbing into bed with him, propping himself up against the digital headboard. He gathered Sam in his arms with an easy strength that thrilled Sam, but that was a promise for another time, and held him close.

“Are you ok with this?” Sam asked with just a hint of worry. He had no context for relationships between programs, and the last thing he wanted was to ultimately push Tron away.

“Whatever you’re willing to give me, Sam, is more than I could possibly deserve,” Tron said breathlessly. “We can discuss the details later.”

Sam tucked his face into the safety of Tron’s chest, his head tucked neatly beneath the program’s chin, the promise of sleep already heavy. “Good night, Tron.”

“Sleep well, Sam. I’ll be here when you awake.”

* * *

Sam woke up feeling refreshed and ready for their excursion into Theta Sector, and he greeted Tron with a grin as the security program handed him a light cycle baton, waiting for him to use.

"Hey, Gemini; you good holding down the fort?" He asked of his program, who nodded with all the serious nervousness of a soldier on his first field mission.

"Yes, I foresee no problems. I'll have an open line of communication with you and Tron should that change."

Sam reached out and clasped his young program's shoulder, tilting his head to look Gemini in the face. He could see the nervous energy in his eyes and could almost taste the tension. "You'll do just fine, you've got this."

"Yes, SamFlynn."

Sam rolled his eyes in fond exasperation. "See you in about a week, Gemini."

He left the arcade with Tron at his side, and the two of them took a running start before activating their light cycles in a show of expanding pixels, Tron taking the lead to guide them forward on their mission.

* * *

Walking through the near deserted streets of Theta Sector was unnerving, but they stayed out of sight, ducking around corners and behind walls whenever Tron got an inkling of another program or search function nearby. It made for slow going, but Sam was grateful for the caution as the last thing he needed right then was to be on some malicious gang's radar; he'd had enough running for his life for the week, thank you very much.

Tron took him to a nondescript building near the center of the sector and a touch to the side of the building opened up the infrastructure mainframe to his growing User perception, revealing no programs inside the building: it was clear for them to begin their work to repair the sector.

They proceeded inside and tucked themselves away in an empty room with only one exit in or out. Sam could create a shortcut if they needed one.

With Tron watching his back, his disk at the ready, Sam dropped lightly to his knees and placed both palms flat to the floor, materializing a helmet to give himself digital readings of the code he was about to work with, and he activated the neural interface with a tap of his finger, sending out tendrils of white light through the floor circuits.

The interface allowed Sam to see the map of the sector in a maze of scrolling white lines, but also immediately visible was the corruption of damaged buildings in bright and jagged red lines. Only about a third of the sector was damaged, but some of the functions damaged were vital to the longevity of the city. Sam tackled those lines of code first, erasing whole sections and rewriting bits and pieces from nothing.

He found echoes of long dead programs fragmented into the damage, reminding him eerily of white shadows from atomic blasts and it left him feeling numb in the scope of life lost since the Grid's inception.

He couldn't let it distract him from his task as the User of the system, so Sam buckled down and dove into the code, repairing what he could and replacing what he couldn't, unaware of the light show he was producing, circuit lines extending out from beneath him in delicate white and green light.

Hours passed before he was done, but to Sam's dismay, he wasn't able to finish the sector from where they were hiding out; they would need to travel around the edges of the sector to finish the job.

"Sam?"

His head was pounding, a massive migraine blooming out from behind his tired, aching eyes, and his hands shook as he closed down the interface, and why was it so hard to breathe?

"Sam! We have to go!"

A strong hand on his arm, just above the elbow, pulled Sam to his feet, and he looked bleakly at the security program, unnerved to see three copies of the program.

"Why are there three of you?" His words slurred out of his mouth, his tongue unable to properly form the words.

Tron swore violently, a dangerous purr echoing in his throat and he picked Sam up like he weighed nothing at all and threw him over one shoulder, carrying the overworked User from the building that was now drawing in too much attention from curious programs that were slowly creeping closer in curiosity. He kept his disk out at the ready, as a precaution, ducking into an alleyway to find another secluded location for them to hide and rest.

* * *

It was more than a little uncomfortable working with Tron when the security program could barely even tolerate his presence, but Sam supposed that he kinda deserved the silent treatment he was getting.

He was still a little off balance from overworking himself, but they were on the last section of the sector that needed fixing, so he could wait for the lecture he knew was coming since he woke up from his pseudo coma four days ago, after having slept for almost a full day.

Sam figured that if Tron spoke to him, or even looked at him more than was necessary, he was going to figuratively explode, and even Sam could figure out that such a reprimand delivered outside of their secured sector in Rho was dangerous to their safety.

Thus the angry silent treatment.

Still, he mused as he put the finishing touches to a maintenance matrix that would compile the repairs to the rest of the sector, he wasn't exactly looking forward to the impending lecture waiting for him back at the arcade.

* * *

Sam hadn't allowed himself to overwork himself to the point of collapse since that first (and only) time, but even a week later, he could still feel the ass reaming he'd gotten from Tron over it.

Tron was just as bad as Alan in worrying over him, but Sam couldn't hold it against the program. Overexerting himself hadn't been entirely his fault; he'd been unaware of just how utterly consuming it was to flex his User gifts on such a large scale, and now that Sam knew better, he'd be more prepared to prevent another such incident.

Still, he put up with Tron's foul temper for the rest of the excursion in Theta Sector, keeping himself calm and compliant, and following Tron's orders without complaint.

Sam had just scared Tron with his little stunt, so he just resolved to fix the problem.

Once back at the arcade, Sam had dutifully returned to his room to get some rest (under orders) and allowed Tron to coordinate with Gemini on the next step.

He was sprawled on his simulated couch, his armour removed and piled in a corner, when Tron made an appearance in his doorway, a glass of liquid energy glowing a faint purple hue in his hand, a gift and an apology in one gesture. Sam smiled at him, waving the program over and shuffling to make room for him.

"I'm sorry I was so harsh," Tron handed Sam the drink, watching as he took a sip that revitalized him.

"I kinda deserved it, you know," Sam took another sip, enjoying the blue raspberry and copper taste. "It won't happen again, now that I know better. Especially with you watching my back, I couldn't go as hard even if I wanted to."

"No, I suppose not," Tron reached over, taking one of his hands in his own, gently running circuit laced fingers across the digits and Sam could only watch, hyper aware of each caressing touch. "Still, I am glad you're doing better now."

"Yeah, not an experience I'd want a repeat of." Tron's feather-light touches to his captured hand was slowly driving Sam to distraction, an electric feedback loop tingling up his arm. From the smug smirk gracing those… _kissable_ lips, the program knew exactly what he was doing to Sam, and that was just too much. He crowded into Tron's space, straddling the program's lap in one smooth motion.

Tron watched him, a dark, delicious promise gleaming in his hooded gray eyes and Sam couldn't resist any longer, leaning down slowly, giving Tron every chance to stop him before their lips touched in a shy, almost chaste kiss that threatened to turn Sam's limbs to goo.

Tron's hands were on his hips, hot through his jumpsuit and his thumbs rubbing tantalizing circles on the glowing circuit nodes there, sending electric shivers crackling up his spine, holding him steady as Sam kissed him again, just as gentle as the first, kissing him back firmly with a nip to his bottom lip.

Sam pulled back just enough to draw in a surprisingly unsteady breath of air, meeting Tron's intense gaze. Being on the receiving end of that particular look did things to him, and he honestly couldn't get enough.

"Hi," he whispered, and Tron's smirk softened into a fond smile.

"Hey."

“Are you sure you’re good with this?” He couldn’t help but ask, feeling remarkably insecure and vulnerable. Tron’s grip on his hips tightened, picking up on Sam’s emotional state and its (to Tron) surprising frailty.

“About a relationship with you, Sam? Yes, I am.” The program leaned up, kissing the corner of Sam’s mouth. “Will it be easy? Likely not, but I can promise you that I won’t leave you, even on our bad days.”

Sam chased Tron’s retreating lips, sucking gently on his bottom lip, an imitation of the nip he’d received moments earlier. “How do relationships even work for programs?”

“While I’m sure that there are obviously differences, I suspect it’s not all that different from relationships among Users,” Tron peppered his face with kisses, punctuating his words. “We’re tactile and affectionate, although kissing is a newer thing.”

Sam chuckled, the sound low and warm. “I heard that story; my dad kissed your girlfriend from the old Encom system, Yori was her name?"

"Kevin didn't get a chance to port her over, of which I am grateful, considering how things ended. She would not have fared well under CLU’s reign." Tron trailed open mouthed kisses down Sam's neck, scraping his teeth over the pulse point to hear Sam's breath hitch in his throat. "But that's the past, and you're my future, Sam."

Sam's grin was decadent and wicked and he slid his hands down Tron's chest, following the white and blue circuit lines, enjoying how the powerful body beneath him shivered at his touch. "Smooth talker."

Tron indulged in Sam's questing exploration, continuing to kiss and nip and suck along the line of his throat at a leisurely pace for several long and enjoyable minutes before rising to his feet, Sam still held firmly in his unwavering grip. He carried the User to his bed, laying him down onto the center of the mattress before slowly pulling away. "Don't start something you can't finish, Sam, and we don't have to finish now; we've got time."

Sam allowed him to pull away, reclining fully amongst the sheets. "Alright, fine. You win this time."

Tron just laughed at him, giving him one final kiss before disappearing down to the main floor of the arcade, leaving Sam flustered and blushing in his wake.

He decided a nap would clear his head; he was bound to have good dreams now.

* * *

Gemini disappeared on another recon mission that would keep him out for a few days, so Sam tried to be productive and worked on his drone design for Tron.

Ultimately, he went with a simple design, keeping the drone about the size of a bit, but he wrote a self replicating algorithm that would allow the bit drones to accommodate to any given situation; cameras could be 'grown', for a lack if a better word, if defenses were breached for later identification purposes; weapons in the form of small, compact plasma energy based lasers packed a powerful punch; and the drones could merge with each other to form a type of intuitive shield, kind of like a Wall spell from those old Final Fantasy video games he used to play as a kid.

Tron was right: insight had come clearly with time away from the problem.

He created and implemented a full dozen drones by the time Gemini came back with good news from Theta Sector; one of the buildings Sam had replaced was a vehicle garage, and a few of the mechanics were more than willing to keep an ear to the ground for information, as well as servicing and providing vehicles for them. All they wanted in return was a restored system.

“This is good for us: getting our vehicles from a reliable third party will take some of the stress off of you, SamFlynn, as you won’t have to create any, and this is an excellent opportunity to foster better relations with the programs, and hopefully in the long term, do away with CLU’s propaganda against Users,” Gemini was excited, it showed in his exaggerated hand gestures as he spoke and in the way his dark eyes fairly crackled with static. “I also got a couple of tips I want to check out.”

“Such as?” Tron asked succinctly.

“There’s a memory hub in Gamma with a lot of User-friendly chatter and there might be an energy bar or a club in Iota or Omicron. I’d need to do some recon to verify.”

“Do it,” Sam said with a sharp nod. “And if you can, get us some clearler intel on some of the red zones. Take your time, and stay safe. No heroics.”

Glee flickered in Gemini’s dark eyes as he grinned unabashedly. “Of course not, SamFlynn; I’ll leave the heroics to you.”

Affronted, Sam turned to Tron, who was hiding his amused smile behind a thoughtfully placed hand. “How the hell did I raise such a smartass?”

“A mystery for the Users, I’m sure.”

* * *

Gemini’s recon was slated as a two week trip, giving enough time for Sam and Tron to set out around their safe little sector and start shoring up defences. Sam made adjustments to some of the buildings and landmarks bordering the sector, adding defensive grids and electronic tripwires and proximity alerts to a security system that Tron controlled from a personalized handheld tablet that Sam cobbled together. He added function controls for the security drones to the device, which allowed Tron remote access to not only the drones but to the other security functions they were installing, and Sam also wrote a complicated password matrix keyed only to Tron’s identity disks.

Sam also started making architectural changes to some of the buildings in Rho Sector, creating a series of apartment blocks and small business type spaces, in anticipation of a future where programs came back, once the population was closer to normal parameters.

He also got the chance to test out his new security improvements when Rho Sector came under attack from a large swarm of gridbugs tunneling into the city from the Outlands about a week (give or take a day or two) after Gemini left. It took some creatiative improvising, some grenades, an overheated lightcycle, and a whole lot of luck to destroy the swarm enough for Sam to locate and destroy the tunnel, but they did it, and Tron rewarded Sam for his ingenuity with a scorching kiss he felt all the way down to his toes.

After that, things started to get a bit busier for Sam and his small family, as once Gemini came back after fifteen days, he and Tron immediately set out for the other Sectors, and over the course of the next five or six weeks, they successfully routed a gang of hostile programs out of a fractured Tau Sector before restoring the sector back to a functional operating status, confirmed Gemini’s tip of a User-friendly bar in Omicron, and successfully rebuilt and restored an almost null Pi Sector while fighting off incursions with a resilient squad of CLU’s Black Guard that wanted the broken sector for themselves.

In quiet moments found whenever possible, Sam pushed his expanding User gifts and started writing programs into existence, mostly with maintenance subroutines and janitorial protocols, since the city was still a mess all over the warring sectors; he needed the help wherever he could get it.

Tron kept him from over exerting himself again, and was not afraid to use threats and blackmail to get his way, utilising Sam’s weakness for his kisses to his advantage.

Sam did note that it was starting to get harder and harder to bypass detection from the programs in the different sectors, with gangs of hostile programs looking for him and neutral ones curious and looking for information. More and more often, Tron was having them move around whatever sector they were in to avoid scrutiny, and Sam felt it was only a matter of time before confirmation of his identity as a User was revealed, and he wasn’t looking forward to the impending civil war.

Neither was Tron, and he was getting twitchy about the increasing scrutiny, becoming even more focused and intense than usual. Sam figured that he was actually spoiling for a fight, just a little bit, but he wasn’t really surprised, as Tron still held remnants of CLU’s reformatting in his system, and he had spent a thousand years as Rinzler; it was bound to leave behind a few souvenirs in his healing psyche.

But they were together, and they could handle anything thrown at them, so long as they had their family and each other.

**Notes for the Chapter:**

> Should only be another chapter, maybe two, before we reach our Star Trek content. Still have some things to flesh out.


	5. Chapter 5

**Notes for the Chapter:**

> We have officially surpassed the length of the original, and haven't even reached all the content I wrote previously! Yay!

A series of explosions erupted around him as he sped away from his pursuers on his lightcycle, dodging fragmented debris as he wound his way through the streets. They were too far into the hostile red zones for any safe haven, so their only hope was to outrun the enemy.

It wasn't Sam’s prefered method of conflict management, but the enemies numbers greatly outnumbered theirs, and those were not odds that Sam would bet on in a straight up fight.

Tron kept pace with him on his own lightcycle, his dark helmet shielding his face from view, and if his circuits had been red, he’d be indistinguishable from his previous identity as Rinzler, but the bright blue was more than reassuring.

The security program waited only long enough for the explosions to to die down before tossing a handful of miniaturized grenades over his shoulder, directly into the path of their pursuers and a glance back showed a spectacular show of staticy fire, derezzed pixels and the sensor readout in Sam’s helmet showed that Tron’s move took out at least five of the hostile programs chasing after them.

He revved his lightcycle, drawing closer to Tron and tapped the comm in his ear. “Hey, we really need to lose these guys!”

Tron’s helmet tilted in his direction, a glance hidden behind dark tinted glass. “There’s still too many, we should split up; think of it like your light cycle Game.”

“Divide and conquer, I gotcha!”

He gave Tron an affirmative thumbs up, watched as the other program returned the gesture and together they veered away from each other, Sam going left down a narrow side street and Tron doing the same on the right, with the gang behind them splitting up to follow the both of them. Sam couldn’t even feel offended that the larger group chased after Tron; the security program was obviously the bigger target in their view.

He brought up a map of the sector to his HUD, speeding his way through the maze of streets and alleys and keeping an eye on Tron’s little blip for peace of mind. He reached down to where he kept a powered down sword attached to his thigh, igniting the blade and keeping it parallel to his side, feeling the heat emanating off the weapon even through his suit.

He had the bare bones of a plan, and yes, it was one of his more reckless ideas, and to pull it off was going to require a little bit of skill and a whole lot of luck.

Once he was far enough ahead of his pursuers and had enough room to work with, he spun his lightcycle into a sharp U-turn, his knee spinning on a dime as the cycle was almost on its side before pushing away from the smooth surface of the street, straightening out and speeding towards the hostile programs now in front of him, his sword held out away from him, ready to strike.

He attacked the programs as he raced by, slashing through several before they even knew what hit them, showering the road in a dazzling display of broken pixels. Taking advantage of the chaos, Sam ducked down another side street, drawing the rest of them deeper into the maze.

He jolted forward across his cycle as one of the red colored programs slammed into his back bumper in the off chance he lost control and crashed. He smirked; he was at his best on the back of a bike. He was rammed again, but this time Sam countered the move by swinging his sword backwards in a downward slash, and the shattering sound of derezz was like music in his ears.

Another hostile program tried again to ram his cycle but Sam instead initiated the cycle’s light ribbon, destroying another two pursuers and the rest of the pack dropped back to avoid the deadly wall of light, and Sam sped away into the next sector, this one a neutral one and safer for him, but he knew that he’d still have to deal the programs chasing after him.

Utilizing the first bit of open space he came across, Sam leapt from his cycle, deactivating it back into a baton that he caught with one hand, putting it back to its spot on his leg. He rolled to his feet smoothly, pulling his disk from its dock with his free hand and igniting it, ready for the coming face off.

As the first pursuing lightcycle came into view, Sam swung and threw his disk, watching as it arced beautifully on target, cutting down the enemy program. He got another as they passed with his sword, deflecting a disk strike with the activated shield attached to his forearm in the same move.

There were only three programs left now, and they were intent on killing him, intent on revenge for their compatriots and because he was a User. They circled wide around him, coming at him from different angles, and Sam knew that he only had one chance to not get his ass killed.

He threw his disk as they closed in, hitting his chosen target dead center through the chest, and he followed through with the momentum of his throw to bring up his shield, blocking the disk strike from the second target while cutting down the third with his energy blade. He kept moving, spinning tightly to bring his blade up, slicing through the back end of the second lightcycle before it passed by him completely, and sending its driver flying to crash in a heap. Sam threw his disk to cut down the program before they could get up and attack him.

Catching his disk on its return flight, Sam stood there for a moment, his breathing heavier for the exertion. His breathing was impossibly loud in the sudden silence following the short battle. He was giddy from actually pulling that off, and he couldn’t keep the stupid silly grin off his face as he looked around at the piles of derezzed code.

Movement brought him back to the present, and Sam saw a couple of curious programs lit up in different patterns of blues and yellows making their way slowly down the block and he took that as his cue to leave. He deactivated both his shield and his sword, clipping the hilt to his thigh and secured his disk back to its dock on his back. He grabbed his lightcycle baton and took a running start, and in moments he was speeding away from the curious onlookers.

A few minutes later, he found Tron at the junction where they’d split up from each other, casually leaning up against the side of a towering skyscraper, waiting for him. Sam slowed down just enough for the security program to recognize him before driving off back to the area of Kappa sector he still needed to repair; his job here still wasn’t done.

It was only a few moments before Tron caught up with him, racing along with him, and Sam had to grin beneath his helmet.

* * *

The last six months passed quickly, a flurry of activity from all corners of TRON City, but slowly the city was being made whole again. It was hard, thankless work, but Sam wasn’t about to give up; this was his home, and so many people were counting on him. He’d successfully restored seven sectors across the city, and the city’s population was growing as former refugees slowly returned from other cities scattered across the Grid, each with stories and rumors of rebellion and uprisings in cities like Arjia and Gallium, and Gemini even brought back a story about a Renegade leading an uprising against CLU’s forces in Argon, taking on Tron’s appearance, which made Sam giddy; Tron’s legend was showing.

Unfortunately, things hadn’t gone as smoothly as he might have hoped, as three sectors were lost to gridbug swarms. Sam needed to figure out a way to keep them at bay, but he was coming up short.

If there was one thing that CLU’s regime had done positively, it was that there had been fewer swarms to deal with.

Sam had been hard at work, either out in the other sectors to initiate repairs on site, or buried in his lab drawing up designs and buildings a slew of drones to add to Tron’s defence network, and necessity in the form of an invading hostile gang had Sam walling off Rho Sector and setting up gates and checkpoints and creating Sentry Units to man those locations, and setting up anti aircraft turrets along the walls.

In addition to a score of more bit drones, Sam had designed and built a pack of Hunter Drones, twenty strong, to patrol Rho Sector. They were not dissimilar to a large wolf pack, which Sam styled them after, both in design and temperament (of course, Sam named them Fenrir) and they were effective enough that Tron was impressed with them, even if their appearance startled him at first.

After all, there were no animals on the Grid, and gridbugs did not count.

Unfortunately, at some point over the last couple of weeks, Sam’s identity as both a User and as the Son of Flynn had gotten out, as well as his location in Rho Sector; although he wasn’t exactly surprised, since he’d been working overtime to secure the arcade and the sector from invasion, but the knowledge of his identity was only going to inconvenience them in the long run.

Anonymity had been one their greatest tools, and now they were constrained by the attention focused on them.

It was so bad that Sam was writing shortcuts beneath the sectors in order for Gemini to leave on his scouting missions.

It was stressing Sam out, to be honest, so much so that he wasn’t looking forward to tomorrow’s mission into the Black Guard-held Epsilon Sector, dread coiling in his gut. At some point in the two week long mission, something was going to go wrong, and either Sam or Tron was going to get seriously hurt.

* * *

Eyes wide in shock, it was all Sam could do to leap away from the lightcycle before he crashed into a red light ribbon blocking his path, and he landed hard on his shoulder, rolling and skidding half a block down the road, the remnants of his lightcycle cascading over him in a shower of white pixel shards.

His shoulder screamed at him, pain lancing through his nerves like a frozen fire, and he couldn’t breathe from the intensity of it. It was definitely dislocated and the armour there destroyed, the suit beneath shredded in fragmented code, allowing the world to see bloody and torn skin that marked Sam as a User.

He rolled onto his front, using his good arm to lever himself into a somewhat upright position, although moving _hurt_. He gasped in shock as his leg protested loudly as he struggled to stand, the pain like frostbite, hot and cold in one sensation and it burned more severely than anything else he’d ever felt along the glowing circuit lines covering his body.

He looked around frantically, searching for Tron, but he'd been separated from the security program a few streets over and he was quickly surrounded by hostile programs lit up in red and orange.

Several pairs of hands grabbed onto him, unyielding like steel bars and just as strong, hauled Sam to his feet and his leg buckled under his weight, leaving him at the mercy of the sneering programs that surrounded him. Even if he could move his arms, his disk was out of reach, and the rest of his weapons were quickly stripped from his body.

He’s dragged towards a tall, powerfully built program in orange and a curious null black, who watched his staggering approach with disdain and loathing. He felt a trickle of blood slide down the side of his face, and watched as disgust flickered in those dark, dangerous eyes of the leader program.

“So you’re the Son of Flynn,” the program said slowly, his voice a strange blend of static and electricity, rumbling like a corrupted file. “Can’t say that I’m impressed.”

“What can I say? People are always underestimating me.” Sam smirked, a cocky grin designed to infuriate plastered across his face.

A crack sounded, sharp and discordant, his head flung to the side as his vision blurred from the force behind the program’s closed fist. Sam paused for a moment to spit out the mouthful of blood from where he bit his tongue before glaring at the program.

“Didn’t realise you were so easy to provoke; my bad,” he said flippantly with just a touch of an eye roll. He wanted to portray that he couldn’t really take these guys seriously, like he thought they were a joke to him. If he could rattle them enough, they might trip themselves up, give him an opportunity to escape and try and find Tron.

Tron was likely to be already looking for him, but that didn’t mean that Sam had to wait for him like a damsel in need of rescuing.

“CLU should have finished you when he had the chance; we’re better off without the meddling of _Users_.” The burly program spat, brow furrowing in his anger and Sam made himself look bored to tears.

“Look, I don’t know if you’ve realized this yet, but without me and my User abilities, there wouldn’t be a system left,” He said as though speaking to a dim-witted child, slow and mildly condescending. “So how about you just let me get on with my work, and you guys can just fuck off back where you came from!”

A backhanded hit made him dizzy, stars bursting in front of his eyes, but Sam refused to make a sound and this time, he spat blood directly into the program’s face, still defiant in the face of much stronger opponents.

A big hand with thick fingers grabbed his throat and lifted him off his feet while he struggled for air, grasping with his good hand at the fingers wrapped firmly around his neck, but the grip was too strong.

Where was Tron?

Like a prayer being answered by divine right, a vibrating disk slashed through the arm holding him up and Sam dropped to the ground, gasping for air as chaos reigned above him. The red-hued programs scattered as another disk sliced through another two bodies, arcing back to its owner, and even from his place on the ground, Sam could hear the deadly purr of Tron’s fury emanating from the security program’s throat.

A grenade exploded not thirty feet away from Sam, and he rolled away from the explosion, grunting in pain as he put pressure on his dislocated shoulder and his vision blurred at the edges from the agony, but he pushed himself unsteadily to his feet, favoring his injured leg as he hobbled to take cover in a nearby alley.

He pulled his disk from his back even as his leg buckled again and he slid down the smooth wall behind him, ready to offline any programs coming after him, but he mostly kept out of the way of the rampaging chaos, as more grenades detonated, the booms punctuated by the shattering of broken code, almost musical in its scope. He heard the vibrating hum of flying disks and energy swords, screaming as lives ended, until eventually, all he heard was a single program breathing heavily in the street, a familiar ticking purr revealing the victor of the fight.

After a few quiet moments, slow, unwavering footsteps stalked towards the alley Sam was hiding in, and he couldn’t keep the pained smile off his face at the sight of Tron highlighted by the streetlights, but his smile faded into uncertainty as he noticed the flickering color of Tron’s circuits from blue to red and back again.

“Tron? Are you ok?”

Tron’s masked head snapped up at the sound of Sam’s voice and his circuits settled back to a safe blue. He stalked towards Sam, stashing his weapons away before kneeling next to the User, his opaque black mask dematerializing.

“You need to be more careful.” His voice was low and controlled and sharp-edged, his gray eyes oddly void of emotion. It was Sam’s sure fire way of knowing when Tron was especially angry or scared.

He wasn’t sure which applied at this moment.

“I’m sorry; it couldn’t be helped,” Sam said in the quiet. Tron’s eyes narrowed and his mouth took an unhappy downturn.

“I wasn’t talking about the crash.”

Ok, so Tron was pissed, and pissed at him. Great…

“I knew you were coming, and I was hoping to buy you some time,” He explained as Tron started looking for his injuries, running his hands lightly across Sam’s body. The shoulder injury was the obvious one that the security program was unwilling to aggravate, but Sam hissed when Tron discovered his busted leg.

“Can you walk?”

“With help, yes. Pretty sure I fractured the tibia in the crash, and it hurts like a sonuvabitch, to be honest.”

“Can you repair the damage?”

Sam shook his head, feeling oddly guilty when Tron’s face fell, dismayed. “Not the way you’re thinking. It’s not like playing with lines of code; there are things I can do to fix things, but it’s a long painful process. I need to get back to the arcade.”

Tron was silent as he thought about their options, running through different scenarios in his head, troubled at the lack of preferable options. “Can you ride a lightcycle like this?”

“Gonna have to; don’t have a light runner available.”

Tron knew he was right; a light runner was preferable to a lightcycle with Sam’s injuries, but they didn’t have one, and they couldn’t even find one in this sector, not without leaving Sam vulnerable, and that was not even an option for Tron.

Slowly, Tron helped Sam back to the street and propped him up against a wall while he activated his backup lightcycle and circled back for Sam. It took some doing, and Sam nearly overbalanced and fell on his face at least twice, but then they were on the road for home, driving with much caution than usual.

If Tron took a more circular route to avoid hostile patrols, Sam wasn’t going to say anything.

Back at the arcade, Sam had to be carried down to his lab to build something like an x-ray machine to check out his leg, and it was hard to do because the pain from making it difficult to concentrate on what he was wanting the medical scanner to accomplish, and since this was the first time Gemini was exposed to User injuries, the poor utility program had to be calmed down and reassured that no, Sam was not offlining, and yes, the damage was repairable, it just took a little extra work.

Sam also created a flexible compound that he could use as a type of cast and gave instructions to both Gemini and Tron on how to set and splint both types of injuries with a warning that he was likely to pass out from the pain, which did nothing to alleviate Gemini’s near hysteria or Tron’s grim-lipped concern.

With Tron at his shoulder, hands in position to pop his shoulder back into the socket, and Gemini hovering over his leg to realign the bones beneath his skin. Both programs were waiting for him to count down and it took everything Sam had to keep himself relaxed when the bones were snapped back in place, but he passed out from the burst of whitehot fire along all his nerves, welcoming the rush of blissful unconsciousness.

* * *

Sam was stuck inside the arcade for three months after the crash; he could have gone out sooner, but Tron was adamant that Sam heal as much as possible first. He also kept Sam on a rigorous physical therapy regimen while he was stuck on forced down time, putting up with all of Sam’s temper tantrums and mood swings as he chafed at the restrictions, and from the lack of any kinds of painkillers.

Although Gemini had made the discovery that liquid energy mixed into a brilliant yellow drink that tasted like lemons and mint acted something like a painkiller, numbing the worst of the pain and temporarily numbing his nerves, too.

Tron didn’t necessarily say anything to Sam, but Sam’s injuries terrified the program, finally revealing to him just how different and frail Users were in comparison to programs, and he recalled the night he met Sam, all those cycles ago, seeing the blood drip down onto the arena floor, and he recalled that fateful night CLU betrayed them, of CLU standing over Flynn before Tron tackled him; he recalled so many fights against programs and bugs that he felt dizzy.

Tron recalled most recently the program strangling Sam, of seeing Sam’s body broken and bruised.

He could have lost Sam on any number of occasions.

Tron could not allow that to happen. He knew that he couldn’t keep Sam locked away here in the arcade, even after he was healed, and that Sam would not rest until the Grid was stable and in full operational status, but concessions would be made.

Details could be sorted out at a later time, but Tron already had ideas about perhaps bringing along a handful of Sam’s bit drones to accompany them during their excursions into the other sectors, to say the least.

He was also going to insist that Sam utilize shortcuts into the affected sectors, and they would travel via light runner from now, with backup lightcycles and lightjets, and even the glider wingpacks.

Tron would do anything to keep Sam safe, he would not fail him.

* * *

Sam glared mulishly at Tron, arms crossed as he sat in his chair in his lab, as the security program stood in the doorway. It had been twelve weeks since the crash, and he was as healed as he was going to be, and while he wasn't completely functional, as his leg still ached at times and he had some minor issues rotating his shoulder, Sam felt that there little to no excuse as to why he couldn't leave the safety of Rho sector to resume his self-imposed mission to fix the Grid.

He hadn’t even worn his suit and armour during his convalescence, instead creating and wearing loose fitting t-shirts and sweatpants, although he didn’t stop at the loungewear, fashioning for himself a leather jacket like his dad’s, jeans and a few hoodies for his comfort.

Tron didn't feel the same way, wanting to keep Sam safe longer, but he also knew that he had to trust the User.

"Fine, we can start planning the next mission. But that will not happen today, or tomorrow," Tron said firmly, running a hand through his hair in an exasperated motion he picked up from Sam. "Gemini's not due back for another three days."

"Fine, we can wait 'til he gets back," Sam conceded, turning back to his work desk where he had a few designs displayed. "But it's time, Tron. There's still a lot of work for me to do."

Tron sighed heavily and walked over to his partner, gently wrapping his arms carefully around his shoulders in a soft embrace, nuzzling against Sam's temple. "I know, I just worry about you."

Sam's smile was a little self deprecating as he leaned back into Tron's hold. "I know, but I am seriously going to lose my mind if I don't get out there and _do_ something. We can be as cautious and prepared as you want, I won't even argue with you."

"You'll take another scan, just as a check up, and when we're out there, you will tell me the nanosecond you feel even remotely 'off', am I clear?" Tron gentled his harsh demands with a feather soft kiss placed high on his cheek bone.

"Sure; it'll be the same as the last two scans you wanted, just so you know," Sam turned his head just enough to kiss the corner of Tron's mouth. "There's nothing else we can do on this side."

"How long has it been since the portal closed?"

"Um, well, I think I've been in here for what- forty five, forty six weeks now?" Sam twiddled his fingers, doing some quick calculations. "That makes it… almost seventy years. That's a lot of time for medical advances, so it stands to reason that when we are discovered, whomever it is should be more than capable of patching me up completely, if they’re going to want to."

"You were being hunted, Sam; we should hope that they are at least friendly."

"I am. The thing about my world, Tron, is that with enough time, old conflicts are meaningless. War will always be a part of the human condition, but the game will have changed. I don't know what will be waiting for us, but you'll be there with me, and there are always negotiations we can do beforehand, and if someone comes into the Grid, we have a hostage for collateral."

"That's rather mercenary of you, not something I expected."

"Can't afford to be naive," Sam closed down the holo display and secured his desk, knowing he wasn't going to get anymore work done today. "But that's a concern for another day."

Sam allowed Tron to gently manhandle him into bed for a nap after his medical scan (which showed no more improvement than the scan Tron wanted the week before) , while the security program kept an eye on the sector through the monitoring system on his personal device, reclined against the headboard with one hand scratching lightly at Sam's scalp as he slept.

* * *

Progress on repairing the rest of the city had slowed considerably over the next two years; the revelation of his identity had been detrimental to both his work on the system and his health, much to Tron’s concerned dismay. Sam had successfully restored all but one of the neutral sectors (being the least dangerous to his safety), three more sectors in the hostile zone, and had completely rebuilt Xi Sector after losing it to gridbugs three months ago.

A few of the neutral sectors had even shifted alliances, becoming pro-User in their beliefs, especially after Sam had met with some of the Sirens running the memory hubs in Gamma, and after repelling a couple of swarms, saving a lot of programs from offlining.

Sam’s victories hadn’t been without cost, however, as shown by the broken ribs he’d sustained about six weeks after Tron had finally given him the green light after his crash, and the broken arm he’d gotten about eight or nine months after that.

Add in the broken collarbone he’d gotten when a volatile group of Black Guard had abducted him during a fight while restoring Mu Sector about eight weeks ago, Sam was sure that Tron was going to veto him leaving Rho Sector for any reason for a while, even with the upgrades he’s made to his armour, reinforcing the pieces around his chest and shoulders, and to the specific pieces where he’d suffered breaks, like his leg and arm.

He couldn’t even blame his partner for his worry; Sam was infinitely more fragile than the programs populating the system, and word was getting around of that frailty. Not to say that Sam was in any way, shape or form weak and couldn’t protect himself, but he did have a disadvantage, and he was approaching the point where he was going to need a doctor from the outside world if he was going to survive.

Luckily, during his forced downtime while recovering from his various injuries, Sam had automated some of the processes of restoring the broken sectors. He’d made some changes to some of Gemini’s core permissions, allowing his utility access to specific junctions where he could insert and port over an automated algorithm directly into the root code of the damaged sector through a type of USB drive he fashioned for that sole purpose.

Doing so allowed Gemini to go out in his stead, and while it wasn’t 100% foolproof, with some sectors needing updates and software patches, it did allow Sam to observe from a distance through his growing perception without the danger of getting hurt himself.

Gemini was also able to secure aid from other programs in the restored sectors to watch his back, and to create diversions if he needed them. Gemini’s friends had also provided him with escape routes when necessary, too.

In other news, Rho Sector wasn’t so empty these days; since Sam had already repurposed some of the taller buildings into living spaces, they’d taken in some of the refugees returning from the other cities. Some of them were security programs that Tron added to his defensive network, patrolling the sector with Sam’s Fenrir Drones, and a squad of mechanics and maintenance programs kept the sector running at optimum levels.

There was one idea that Sam was mulling over in his head, not yet talking it through with Tron, if only because he wasn’t sure if he (Sam) was ready yet. He’d been playing with the idea of checking out his father’s old house in the Outlands, maybe for some plans or whatever, but the ghost of his father still hung heavy sometimes.

Tron was nothing if not observant, though, and the program cornered him one day in his room, corralling him onto the couch with Sam half lying on Tron back to chest, arms wrapped around the User and legs entangled together.

“What’s on your mind, Sam?” Tron asked quietly, listening to Sam’s breathing and the beat of his heart.

“Just…” He sighed, long and drawn out. “Ghosts of the past.”

“Such as?”

“Dad’s safehouse, in the Outlands. I think I might wanna go and check it out, see if there’s anything left.”

“And you’re not sure?”

Sam shook his head, running his fingers along Tron’s arms around him, idling at the glowing circuits that brightened with his touch. He knew that Tron felt the light touches, that the sensation was almost ticklish, and if the mood was right (which it wasn’t), could also be very erotic.

“If you allow me to plan the trip, we can go when you’re ready.”

Sam tilted his head to look at Tron, noting the pensive expression. “Really? I thought it’d take more of an argument, honestly.”

“It’s your father, Sam. It’s important, to the both of us, I’m thinking.”

“Thank you, Tron.”

* * *

Tron delayed the trip to the Outlands for almost six months before he was satisfied that they would be safe enough to leave the city entirely, while defending Rho Sector from the last of CLU’s Black Guard and overseeing the defences of the neighboring sectors and his security network. He planned for trouble getting out of the city, and for trouble getting back in once they were done. He vetted and handpicked a squad of specialized programs to accompany them in the trip, securing their transports and gear as he went. He coordinated with Gemini and a few of their Siren allies to accommodate their absence for the few days required for the trip, and Sam let him do it to his heart’s content, knowing that being away from the City unnerved the program.

Sam worked around him, sending Gemini out with system updates and sector upgrades, and generally keeping himself confined to either his little lab or his room, trying to stay out of the way and to not aggravate his old injuries. Despite being as healed as he could be without an actual doctor and proper medical treatment, Sam still felt the aftereffects of his broken bones and lacerations. His abduction eight months ago, had left behind some scars aside from the broken collarbone, including a concussion and a very serious laceration down his hip from a poorly deflected disk strike.

He’d almost bled out from that wound, but thankfully, once he’d been brought back to Rho Sector, Tron and Gemini had patched him up and an IV of energy had smoothed and quickened the healing process.

Still left behind quite the jagged scar marring his skin.

But now they were ready to go to the Outlands, first thing in the morning, and Sam was unable to relax, filled to bursting with an excited sort of nervousness. He’d only been in his father’s safehouse for a few short hours that night a long time ago, and Kevin Flynn hadn’t shown him anything that wasn't out on display, like the Go board, or the simple furnishings.

He didn’t know what he was going to find, if there _was_ anything, and that scared him a little bit.

He paced about his room, unable to calm his nerves, until a firm hand grabbed his arm and halted his steps. He looked up at Tron, and the program guided him gently to his bed in silence, removing his armour with diligence and care before laying them both down beneath the sheets.

Tron rolled over to cover Sam’s body with his own, caging the User in between his arms before leaning his head down to kiss him softly. Sam sighed at the soft touch of Tron’s lips on his, bringing his hands up to glide over his flanks as he deepened the kiss, sucking on Tron’s bottom lip and enjoying the purr the action brought out.

Tron pulled away from the kiss to slide his nose along the side of Sam’s jaw, peppering the skin with tiny kisses as he dipped down his neck to suckle at the pulse point there. He shifted his weight to lean on one arm, allowing for his free hand to trail down Sam’s chest and stomach until he held onto his hip, his grip just shy of bruising, the touch igniting a deep pool of heat low in Sam’s belly.

Sam’s hands weren’t idle as he traced patterns down the length of Tron’s spine, repeating specific moves whenever Tron shivered or his breath hitched in his throat, licking along the shell of Tron’s ear as he did.

“Sam…” Tron’s voice wavered, like he was seconds away from losing control. “Tell me if this isn’t what you want.”

“Always want this with you,” Sam was already breathless as he thrust his hips upwards, grinding against Tron’s thigh, seeking delicious friction.

“Then show me what to do.” Tron’s legendary control was hanging on by a thread, his circuits glowing a bright purple where Sam touched him with incessant fingers.

Sam obliged by derezzing his suit, the black material slowly dissolving until he lay naked under Tron’s fiercely intense gaze, the program’s eyes glowing a bright blue from the pupils. He knew from previous makeout sessions that programs weren’t equipped the same way Users, anatomically speaking, but there were still a lot of things he could do to Tron to push him into overloading his system.

He took one of Tron’s hands in his own and guided the program to take hold of his already leaking erection, gasping at the intense sensation of hot circuits tracing the delicate skin, and he adjusted the hold and gave himself a few tugs to show Tron the motions.

Tron was nothing if not a quick study and he soon had Sam twitching and squirming as he tested different pressures and speed, repeating motions that wrung moans from deep within Sam’s chest, dipping his head to lick at the sweat beading along his neck, biting at the delicate flesh behind his ear, and all Sam could do was hold on, clawing desperately at Tron’s back before sliding his hand to tangle in Tron’s hair.

“Come on,” Tron murmured in his ear, voice wrecked and shaking, shifting to slide his unoccupied hand to clasp Sam’s, tangling their fingers together. “I’ve got you, Sam.”

Sam bucked up into Tron’s hand, shaking as he neared the cliff edge of his orgasm, tears slipping from the corners of his eyes, moaning into Tron’s as he kissed him deep, sucking on his tongue as he rocked upward.

The pressure in him builds and builds until all he can feel is Tron everywhere; long fingers wrapped around him giving him intense pleasure that he started to see white stars; their hands entwined, the sole focus keeping him tied to this plane of existence; the heady feel of Tron’s lips and tongue tracing symmetrical patterns along his chest and neck.

White light filled Sam’s vision as he tipped - _finally_ \- over the edge, and he came, spilling over Tron’s fingers and his own stomach and static filled his ears for a few seconds before he started to come down from the high. Sam blearily looked at Tron and found him just as wrecked as he felt, quivering from the feedback loop from the overload to their circuits.

Tron dropped his head to rest his forehead to Sam’s, their breath mingling together as they regained some level of composure. Sam shivered as his overheated flesh tingled in the cool air, and he petted the skin and circuits at the back of Tron’s neck, marveling as the program shivered in response.

“Are you alright? Was that alright?” Tron asked him, voice cracking in an overwhelmed purr, the ticking sound thrumming from his chest. He reached over the side of the bed to grab at one of Sam’s shirts to clean away the mess.

“I’m more than fine, Tron; that was… unlike anything I’ve experienced before,” Sam chuckled as Tron looked at him inquisitively. “In a very good way, I promise.”

“Good,” Tron murmured, allowing himself to collapse next to Sam, one arm draped carelessly across the User’s middle, the purr in his chest hitching up a notch as Sam started to gently scratch at his scalp. “Are you relaxed enough to sleep now?”

Sam laughed, even with a sleepy grin across his face. “Was that the point of you coming up here?”

“One of my motives, yes.”

* * *

They took three light runners out into the Outlands, with Tron in the lead as he drove the vehicle through the rocky terrain. The other two runners carried a total of six programs, their backup on the off chance that they would run into trouble out here in the wilderness, be it from gridbugs or hostile factions hiding out in the wastes.

The long drive was done in silence, the mood as serious as it was solemn. Sam stared out at the dark terrain, watching quietly as lightning flashed amongst ever-rolling storms off in the distance. Today, in light of where they were going, he wore the replica of his dad’s leather jacket over the top of his suit and reinforced armour, fiddling with the zipper constantly.

Shortly before they reached the safehouse and the hidden door of the makeshift garage, Tron reached over and pulled his hand away from the zipper, holding it firmly in his grip.

They left the vehicles outside with a guard of three, one for each of the light runners and stepped into the elevator, riding it up to the open concept living room. It was immediately obvious that the place had been visited at least once after he’d left that night; if Sam had to guess, it must have been CLU, following his trail back to the safehouse.

Some of the books along one of the shelves were thrown about, the decorative pieces on the dining room looked to have been thrown about in a fit of anger, and the Go board was on the floor, the black and white pieces scattered across the floor.

Sam looked around the room with a heavy, drawn out sigh, the air rattling in his lungs as he slowly picked his way through the debris. He bypassed the room his father had given him that night, knowing there was nothing of value in what was the equivalent of a guest room, instead going down the hall to Quorra’s room.

Sam’s hand shook as he pushed open the door, revealing an unmade bed, a vanity table filled with knick knacks that his father must have created, and a slew of books scattered around the room in neat piles. Sam recognized most of them as literary classics, bringing a sad smile to his face as he remembered Quorra’s love of reading and old books, specifically those of Jules Verne.

He paged through some of the books, finding only a couple of data disks, but the thin hexagonal files only held Quorra’s personal thoughts, much like a diary.

His body shook with his grief at the sight of the ISO’s excitable nature, her brilliant smile lighting up her face on the display, tears falling freely down his face as he listened to her words detailing some of her daily life and old memories that she had wanted to talk through.

He closed the files and slid them into a secured pouch at his belt before leaving the room. The programs accompanying them lounged in the main room, sitting comfortably on the couch and talking softly amongst themselves, but Tron was outside on the balcony by the energy pools, leaning against the railing as he gazed upon the city skyline.

Sam opted to leave him be for the time being, making his way to his father’s room. It was just as bare as the rest of the safehouse, so unusual for Sam as he remembered his father’s spaces always being cluttered, either with pages of notes or books or toys from his games. Seeing the sparse room just brought it into focus for Sam just how long his father had been trapped out here.

Kevin Flynn had survived in the Outlands for close to a thousand years with no one but Quorra for company, adopting a sparse but militant Zen like philosophy in order to survive the circumstances of CLU’s betrayal.

It did not give Sam any faith that he was going to find anything here.

Digging through the drawers of the dresser, Sam stumbled upon his dad’s jacket, falling to his knees and bringing it close, he could still smell him on the old leather. He was trembling, both from nostalgia and from the memories of seeing his father again.

It felt like a long time before he was able to stumble back to his feet, looking around the empty room, wondering just where his father would have hid anything. He reached out with his senses, feeling Tron’s code and that of their guards, and cast about the room, searching.

There, a small compartment built into the unfinished rock of the wastes. He maneuvered around the password mechanism locking the compartment and the small unit extended out from the wall, revealing a handful of datafiles similar to those he’d found in Quorra’s old room.

He sat on the bed, staring at the files, unable to open them. He couldn’t do it;couldn’t stand to hear his father’s voice again. Not yet, not now.

A familiar presence sat down next to him and wrapped an arm around his shoulders in a one arm embrace. Tron leaned in and pressed a kiss to Sam’s hair as he cried, his body trembling as he clutched the data disks holding the last pieces of his father.

“I can’t do it, Tron. I can’t look at them, not here,” Sam whispered through his tears, his voice cracking, tight in his throat.

“It’s ok, Sam,” Tron reassured him, reaching over to wipe away the tear tracks. “They’ll still be here when you’re ready.”

“When I do look at them, I want you there with me.”

Tron nodded, kissing him again. “Of course, Sam.”

“There’s nothing else here. We can leave whenever you want.”

They didn’t stick around for too much longer, just long enough to gather up a few trinkets to bring back; a bunch of the books, the Go board, a few odds and ends. Sam kept the datafiles on his person, but the rest of it was packed away securely into the light runner.

The trip back into the city was uneventful, and just as quiet as the trip leaving, but Sam felt… free, maybe. Like a weight had been lifted off his shoulders, even though he hadn't been able to look at his father’s disks.

The trip was still a success, and Sam felt that maybe, just maybe, he would be able to put some of his ghosts to rest. Curiously, as they crossed the reinforced borders of Rho Sector, activity buzzed through the streets, and Tron’s comm line chirped at him. With a questioning look to Sam, the security program materialized his helmet in order to receive whatever message was waiting for him.

“Gemini’s returned and he has something for us. Refused to give any details until we were there in person.” Tron said as his helmet retracted, a troubled look clouding his face.

“What do you think it could be?” Tron shook his head, tightening his grip on the steering wheel. “There’s no telling; could be any number of reasons. He did not sound like he was in any distress, though.”

“Small miracles,” Sam sighed, leaning back in his seat. Tron’s mouth twitched upward into a small smile despite his best efforts.

“Indeed.”

At the arcade, Gemini was waiting for them in the front of the building, not even waiting until Sam had properly dismounted from the light runner before trying to drag him off into the arcade, pulling on his arm to move him along faster.

Down the stairs into the basement, Sam managed to regain his footing and pulled Gemini short in his tracks, Tron at his back as he regarded his program with concern. “Slow down,Gemini; what’s going on?”

“There’s a message!”

Shock numbed his nerves, freezing Sam where he stood in the armoury. “What?!”

“I just got in myself; I was only down here for a replacement lightcycle,” Gemini babbled, excitement lighting up his circuits with excess energy. “But the terminal pinged in the portal room, so of course I had to check it out.”

Sam and Tron shared a look before Sam bolted into the portal room, eyes scanning the monitor above the terminal, and there it was: an open chat window, a single message displayed on the screen.

_/Hello?/_


	6. Chapter 6

**Notes for the Chapter:**

> For those who have read the original over on FF.net, at lot has changed.

James T. Kirk had never been one to sit still or take it easy when life threw him a curveball, if essentially being brought back from the dead could even be called a curveball. To be honest, he should have still been in observation over at Starfleet Medical, but current events had apparently changed things down to the molecular level for him, although even the Admiralty outside of a convalescing Pike knew the specifics.

After the events brought about by Khan and Marcus six or seven months ago, the Enterprise and her crew were grounded on Terra (or Earth, as some traditionalists preferred) at least until the ship was repaired and refitted for its next mission, which was an extended five year deep space exploration mission.

Pike had survived Khan’s attack on the council by the skin of his teeth and through the skills of some seriously fast acting medics and campus EMS units, but none of the senior staff of the Enterprise had found out until the Vengeance was crashed into the San Francisco Bay and Khan was sealed away with the rest of his Augments after his blood was used to revive Kirk from dying during his stunt in the warp core.

To be frankly honest, Jim would do it again, because the Enterprise and her crew were both his home and his family.

And like Khan, Jim would do anything for his family.

But there were some consequences that Jim was going to have to learn to adapt to and live with, as Khan’s blood hadn’t just revived him, it had changed his DNA to an extent. After rigorous testing that was being kept sealed and extremely confidential, McCoy had determined that Jim would likely live as long as Vulcans, which was about a hundred years longer than the average human lifespan. Khan’s blood had also eradicated most of Jim’s allergies (caused by being born on an unprotected shuttle after Nero killed his father, the shuttles in those days didn’t have the appropriate radiation protection), and changes had been made to his musculatory system, giving Jim a boost in strength to twice that of an average human male.

He also healed faster than was normal for humans now, which is how he was already free from Medical and the torture that was physical therapy; dying from radiation poisoning had seriously messed up how his body worked.

In all, he wasn't an Augment like Khan, but he _was_ genetically enhanced.

That wasn’t to say that he didn’t have a lot of work to occupy him; Starfleet was still struggling, if only marginally, after the Narada Incident had decimated their numbers, but recruitment had been up in the last two years, so with their forced downtime, those members of the Enterprise crew officers not assigned on short term reassignments were teaching at the Academy, or subbing in for other officers elsewhere.

Most of the Enterprise crew were sticking close to home, so to speak, taking small assignments either at the Academy or on small missions with starships within the solar system, with several volunteering for cleanup and rebuilding efforts from the damage Khan had caused when he crashed the Vengeance into the Bay. A small few had taken permanent reassignments, like Carol Marcus had when she took over a research position on the Mars space station. Jim wished her, and the others, all the luck in the world.

Scotty was practically living in the Enterprise as he personally oversaw the repairs and refit, having been reinstated as Lieutenant Commander and Chief Engineer, fully supported by both Kirk and Pike. He also spoke at the occasional engineering seminar as a ‘vacation’.

Whizkid Pavel Chekov, after an extended visit to family back home in Russia, started teaching some of the introductory maths classes required for some of the science tracks, while participating in a couple of research labs that Jim didn’t particularly care for, and was a TA for several of the advanced mathematical and navigational courses, including Stellar Cartography.

Jim didn’t know how the kid had the energy, but he encouraged him all the same.

Sulu had opted for teaching some of the piloting classes, as well as some botany based sciences courses. He also regularly went to the research base on Mars (not the orbiting station Carol had gone to) to participate in some experiments there, and from the reports that Jim had managed to sneak a peek at, things were going exceptionally well.

Uhura was not only a staple in the Communications Division, she was also teaching a slew of linguistics and language classes. She was also instrumental in some of the Enterprise refit installations, working for days at a time with Scotty in order to ensure that her department was up to her high (effective) standards.

Spock was insanely busy these days, running all over the place as he worked with his father at the Vulcan Embassy, while teaching several of the sciences classes and an intergalactic ethics seminar that was crazy popular (Jim had watched the footage of the first one; Spock was an amazing public speaker). The half Vulcan was also running several of the science labs, with about half of the Enterprise’s stranded blue shirts following him around akin to baby ducklings.

McCoy was practically a permanent fixture at SF Medical, either in the research labs or in the OR. Starfleet had magnanimously allowed civilian casualties to be treated on campus whenever possible, and the Enterprise CMO had taken the lead there. Whatever down time he had was sharing vidcalls with his daughter Joanna, or in writing a staggeringly high number of publications that Jim honestly couldn’t fathom how the good doctor could find the time, between his CMO duties, his responsibilities in SF Medical, and the arduous task of keeping Jim out of trouble for longer than five minutes.

But then again, the Enterprise is definitely crewed by a complement of insanely smart child geniuses (practically all of them), so it really wasn’t so surprising that the best crew in Starfleet was so singularly occupying their time after yet another tragedy.

Keeping busy always worked as a coping mechanism for all the crazy shit that happened at least three times more often for the Enterprise crew than the rest of the fleet.

Just another Tuesday.

But Kirk had not been able to join his fellow geniuses in their endeavors until just recently, when he’d been released from Medical ahead of schedule, and since that moment six weeks ago, he’d been mired down with meeting after meeting, debrief after debrief, with everyone from every single remaining member of Starfleet Command to the dozen of different press organizations of the Federation, to even Section 31 (albeit with ‘new management’) and he’d only responded to all enquiries with the aplomb befitting an experienced, dedicated starship Captain only doing his job for the good of the Federation.

Basically, he bullshitted his way through the press ops and debriefs and refused to cooperate, or even speak with Section 31 entirely.

Nevermind the staggering amount of paperwork he found himself slapped with; it was enough to make him want to tear his hair out.

But sadly, Jim’s classes that he was slated to teach weren’t until the next semester, still another month away, and the security teams from the Enterprise were already covering his usual combat classes for this semester, so Jim found himself at odds with himself, with a lot of excess time on his hands.

So here he was, wandering around the streets of Central City, only a few hours away from San Francisco, having almost literally dragged Bones out of SF Medical with him on an adventure as he called it.

Mostly to get away from all the paperwork.

This part of the city hadn’t been touched for decades, it looked like, as the streets themselves were still made with oldschool asphalt, and the buildings, stretching out across the enumerable city blocks, were all in some state of disrepair and rusted debris from years and years past.

If Jim had to guess with any kind of certainty, this part of the city had been condemned at least a century ago, if not longer, and for a moment he was awed at the perseverance of the architects of the late 20th century. It was like walking through a piece of history, of a time from before the last great wars that had haunted Earth’s history.

The Eugenics Wars and the following World War 3 of the 21st century had been a dark part of history that even today still held mysteries lost to time. The Eugenics Wars had been damaging on a number of levels, eventually leading to the creation of Khan’s Augments and there had been a slew of corporate espionage and cyberwarfare until the Augment rule of the planet, leaving the casualty list pretty low in comparison to others large scale wars, but it was the nuclear warfare of the third World War that had lost future generations their history. There were years missing from any of the archival records, where it was only speculation and the odd archeological dig that gave them any sort of insight into those missing years.

To this day, they still didn’t have a clear account of what led to those wars (although there were plenty of theories and conspiracies alike), nor did they have a true estimate of how many lives had been lost, though there were theories that it numbered into the millions, at a conservative guess.

“The hell are we doin’ out here, Jim?” McCoy griped as he trudged along the empty sidewalk next to him, side-eyeing the ruined brick-and-mortar around them. “There’s nothin’ out here.”

“Just taking a walk, well away from the stress and fuss of HQ, Bones.” Jim smiled disarmingly, nudging Bones with a shoulder bump. The two men were dressed casually in old jeans, t-shirts and Bones sported a thick wool trench coat to Jim’s own fur-lined leather jacket. “Besides, you needed a break just as much as I needed to get away from the Admiralty Board; can’t have you working yourself to death, now can I?”

McCoy grumbled halfheartedly with an eye roll, but he didn’t deny the claim, which was as good as an agreement.

Jim’s ever present smirk fell as they rounded the corner at the end of the block, his bright eyes drawn inexplicably towards a mostly demolished building across the street. There was an old sign broken and half buried beneath the rest of the rubble (Flynn’s, maybe?) but there was something about the way the ruins lay that spoke of something other than natural wear and tear.

He crept closer, skirting the edges of the broken walls that barely came up to his knees, leaving a clear view of the foundation and layout. Walking through what should have been the front entrance, Jim scanned the ground carefully.

Yup, there it was. He knelt down and dipped his hand between a few of the larger pieces of debris, pulling out metal casings. They tinkled, bell like, delicately in his hand as he scanned the rest of the immediate area.

“Jim? What are you doin'?”

“Found a mystery, Bones; there was a fight here at some point.”

“And it matters now how?” “Doesn’t really; just curious.” He grinned, though it was a little too sharp and shark-like for casual. “Got a feeling, though.”

Uh oh. Jim’s ‘feelings’ usually turned out to be something unexpected and spectacular in equal measure, so Bones was not about to dissuade his friend, knowing full well that this new ‘feeling’ would eat away at Jim’s mind until he was driving himself and Bones figuratively crazy. It was better to let Jim attempt to solve whatever had caught his attention.

“Lead the way, kid.” Bones’ sigh sounded put-upon but Jim knew it was affected, not a reality; Bones being dramatic, as per usual. “Walk me through it.”

“These,” Jim showed his friend the bits of metal. “Are bullet casings. The way this building fell also shows signs of a controlled explosion, though it’s likely the fragments are gone to time.”

He moved slowly through the rubble, looking curiously at some of the more intact pieces of machinery littering the floor. “If I’m not mistaken in my history, these machines are gaming consoles… um, first generation if I don’t miss my guess.”

“First generation… that’s like two hundred fifty years, if not older.” Bones scowled fiercely at Jim’s obvious surprise. “My grand-daddy loved that kind of old tech, even had a working first edition Pac Man arcade console.”

“You never cease to amaze me, Bones,” Jim laughed, eyes bright with excitement. “But that does lead to the obvious question: Why would an arcade be attacked?”

“What was around here two hundred and fifty years ago?”

Jim shrugged, nonplussed. “Honestly, I’m not sure. I think the city was big on software development and the advent of computer sciences, but there were plenty of other places in the world that did the same around then. I’d have to dig to find out anything concrete.”

“Let’s see what else we can find here, then.” Bones moved deeper into the ruins of the demolished building, removing his trench and laying it over one of the remaining walls, and Jim’s ever present grew affectionate.

“You’re the best, Bones.”

“Yeah, yeah, I know.”

The next couple of hours of digging through the rubble showed more evidence of a violent gunfight, with more casings from at least two other types of guns, more explosive fragments throughout the building, and the remains of at least half a dozen bodies, though not much remained beyond bits of bones and primitive armour that Jim recognized as kevlar, a synthetic material used as a counter to ballistic weapons. There were suspicious rust colored stains near one of the back walls, and it took some digging to discover what remained of a hidden door leading into a basement of some sort.

Jim knelt down and ran his fingers over some well worn grooves in the concrete and looked at the destroyed gaming console still buried under a huge chunk of wall. The game acted as a kind of hidden door, it looked like, and was riddled with bullet holes. Well, what he could see of it.

“So, what’s in the basement? Maybe the cause of this attack is down there,” Jim mused, standing to start digging down. His increased strength was a boon here, otherwise he would have never been able to do this without alerting any kind of authority, and he wasn’t ready for that, just yet.

He knew that Bones would keep this quiet if he asked, but it honestly depended on what he found in the basement. He had the feeling, though, that whatever was driving his curiosity was somewhere down there, hidden in the dark.

Bones helped him dig out the rubble, revealing a hidden staircase, narrow and filled with dust, and completely dark. Jim removed a penlight from his jacket pocket, lighting the way as they carefully descended into the basement. It looked like two small rooms, a set of old wooden double doors stood locked with a rusting length of chain and a big padlock that looked like it would need to be cut through.

There was also a body, propped up against the doors, nothing more than a dried husk, sealed for over two hundred years and the collapsed stair had protected the body from deteriorating completely. The clothes it wore were nothing but rags at this point, but Jim’s light shone off a cracked pair of glasses and an old fashioned pistol lying next to the body.

Bones was right next as he looked at the body, grim lipped. “Looks like whoever this poor bastard was, he died protectin’ somethin’.”

“I was thinking the same thing; whatever it was is behind that door.”

They didn’t have anything that could cut through the padlock on the door, and Jim didn’t want to break down the doors in the off chance they damaged or destroyed anything in the next room, so he went back to ground level, grabbing and dragging a particularly large chuck of broken wall, smashed the padlock off with a few well placed hits, utilizing his enhanced strength.

He hesitated briefly, hand on the door handle, looking again at the corpse on the ground. “What do you think we should do about the body?” Bones shrugged, holding the light for Jim. “Depends on what you find in there, kid, and what you wanna do about it. I can make arrangements, whatever you decide.”

Fair enough. That left Jim with the moment of truth: what was behind the secret door?

It was dusty, and his footsteps left tracks in the dirt as he stepped into the small room. It was nearly empty, with a rotting couch against the far wall, an ancient cork board filled with indistinguishable bits of paper, long since rotted away. To the left was some sort of apparatus, almost as tall as Jim was. A quick inspection told him that he could probably restore it; some of the plates and rods were rusted, and the delicate crystal lenses likely needed replacing, same with a bunch of the wiring, but it wasn’t beyond his capabilities. It would need time, patience and a delicate hand, though.

A sound, a low hum, tickled his eardrums from the other side of the small room, drawing Kirk’s attention away. Curiously, a large computer took up the most space, about as big as the desk in his ready room onboard the Enterprise, and surprisingly, it looked like it was operational. Despite the literal centuries of dust, the vents for the exhaust fans were unclogged and fully functional. It looked like the computer was running on its own power, as there was nothing connecting it to the ruin that sheltered it.

Very carefully, Jim ran his hand over the top of the glass top, revealing a touch screen keyboard as the computer came out of hibernation. He wiped away piles of dust and dirt to view the screen and a quick look at the operating system (something called The Grid) was running quietly, and that at one point there had been some significant damage. The damage had somehow been repaired over the long years, a fact that piqued Jim’s curiosity even more.

“...I think I’m going to see if Scotty can transport this onto the Enterprise, to the Captain’s quarters maybe.” He said softly, voice low but thick with anticipation. This was a puzzle he wanted to solve, but he didn’t want to necessarily inform Pike of it just yet.

“You sure that’s a good idea, Jim?”

“It’s an entirely closed system, Bones,” Jim said, tapping away at the keyboard. “This thing isn’t even hardwired for a wireless connection, making it completely safe in regards to our Silver Lady.”

“How are you going to get it on the ship, then?” Bones was peering over his shoulder, squinting at the screen. “The Admiralty is going to throw a fit about this, you know that, right?”

“I’ll get Scotty on it; he’s discreet, and I’m not telling anyone about this yet. I wanna find out more first; like who is the dead guy? And what is in this system that he wanted to protect? I’ve never seen anything like this, Bones. This is computer programming at its finest; even with today’s technology, the programming I’m seeing here is already more advanced, more streamlined, somehow more… organic? I’m not sure, but I wanna find out more before I bring this before the rest of Command.”

“You should give Pike a head’s up, at least.”

“Yeah, of course. He’s always been good to me,” Jim retreated from the computer and pulled out his comm unit, intent on making the arrangements with Scotty. “He’s never begrudged me before.”

It didn't take long for arrangements to be made to very carefully transport both the computer terminal and the mystery machine back to the Enterprise, and Scotty was fine with keeping the acquisition on the down low since there wasn’t any danger to the ship’s systems. His Chief Engineer was just as curious as he was, intrigued by the prospect of what could be considered ancient technology from Earth’s lost history.

It would take a bit over three days before the terminal was ensconced in Jim’s personal quarters aboard the starship, but both he and Scotty decided that until they knew what the other apparatus was, and how it worked, it would stay in a small Engineering lab on the Engineering deck, especially since it needed a lot of work to be functional again.

Scotty was helpful in transporting the mysterious corpse to an isolated autopsy room in the medbay for Bones to investigate at his leisure. The autopsy room would keep the body in stasis for as long as he needed, and it was private enough for him to claim a research project (which wasn’t a lie, either).

Jim also brought Spock in on the discovery and his intent to investigate, and while the First Officer had concerns, Jim was able to placate him enough that he allowed Jim to continue without informing the Admiralty Board. Jim was under the impression that Spock was just as curious about the whole scenario as he was, but was much better at concealing said interest. Besides, this was all in the name of the preservation of history and science.

Pike, however, had just watched Jim as he reported his findings with a well worn look of fond exasperation, clearly used to Jim’s lack of protocol, but he too was interested in the results of Jim’s investigation, so the Admiral let him be. He also promised to smooth over any ruffled feathers that were bound to arise when Jim was ready to bring his findings to the rest of Starfleet.

When the spring semester of Academy classes started, Jim only took on his old self defence and combat classes, because he found himself mired deep in research regarding the origins of the terminal and repairing the other machine, of which he and Scotty had concluded that it was some type of laser, though its use was still a mystery.

The only clue they had of the laser’s function was an activation screen on the terminal that asked if the aperture was clear. Wisely, they decided to leave the laser alone, with no unauthorised testing, until they could get more information.

Bones made some headway with the corpse, but not as much as he’d have liked. He was able to determine that it was a human male of approximately sixty years at the time of death, and the cause of death was from a series of five gunshot wounds to the torso. He’d used some facial reconstruction programs to give them a face, and he’d been able to do a tentative match to an ancient employee record of one of the big computer software companies of the time, Encom.

Jim was able to corroborate that with his own findings a month or so later, determining that Encom had a pretty turbulent history back in the late 20th century. Records were spotty at best, but when combined with the arcade called Flynn’s, Jim was able to find out that at some point in the 1980s, a man named Kevin Flynn had taken control of the company and turned it into the birthplace of cutting edge technology for the time period. He’d mysteriously vanished without a trace within the decade and about twenty years later in the early 2010s, his son disappeared much the same way, shortly after some amazing advances had been made in a swathe of the science fields, including medicine and genetics.

The small fact that the Eugenics Wars had erupted within a decade of the son’s disappearance made it seem like there had been a coup of some kind, and the Flynns had been killed, and what little evidence Jim could find supported that theory.

There was nothing about the mysterious terminal or the laser in any of records left behind by the long-gone Encom, however, so Jim was going to have to dig in the memory files. He hadn’t wanted to mess around too much with the terminal just yet, but with only six weeks left before the Enterprise, now fully repaired and refitted for its upcoming five year mission, Jim was out of time, and he didn’t want to surrender the terminal to the scientists on campus.

So there he was, settled comfortably in his quarters about six weeks from departure sitting in a comfortable chair at the terminal, ready to do some digging.

Tapping away at the keys, Jim couldn't help but marvel at what he was seeing on the screen; there was no way to really describe it, and he’d never seen anything like it before. If he was one for being whimsical, he’d have said it was sort of like watching a small ecosystem. The operating system, or the Grid, was rife with activity, but curiously, it seemed like all the functioning processes were slowed. Computers normally operated with processing speeds far greater than most beings could process information, but evidence in the data logs showed Jim that those processes had been deliberately slowed at some point.

He also found that the laser was attached to a type of function labeled as a portal; a portal to what? A portal _for_ what? The more he looked, the more he had questions. The hours ticked by as he scanned the code, although he didn’t know anything about the system to accurately identify what he was seeing. There were thousands and thousands of programs in the Grid; it almost appeared to be some archive, maybe? Jim couldn’t be sure just by looking, and he couldn’t seem to find anything definitive.

He almost missed it, it was so innocuous, but he stumbled onto an active communications program, but this was a closed system, so why would there be an open program with nowhere to send a signal to? Clicking into the program did nothing to answer any of Jim’s growing questions, but the other end of the relay led into the Grid, so maybe it was a method of communicating with a VI or maybe even an AI.

Best way would be to test it out with a simple message.

_/Hello?/_

A few minutes passed before there was a reply. _/Hello. How did you find this terminal?/_

_/It was sealed in a hidden basement under a demolished building. Who are you?/_

_/First tell me the date and who you are./_

Didn’t computers, even back in the late 20th century, have a chronometer, like automatically installed when built? What a strange question for an AI, even an advanced one, to ask. Still, Jim didn’t mind the enquiries, but it might be a good idea to let Pike know he’d essentially made First Contact. He sent off a message to the Admiral from his PADD, then sent one to Spock and McCoy, since both men were invested in what he could discover. Spock replied that he would be able to join Jim in approximately fifteen minutes, while Bones wanted to be informed if there was any possible news on the corpse. Pike just told him to use his ‘genius head for once and be careful’.

_/I asked the question first, but I’ll give you an answer: My name is James Kirk, and it’s the year 2260./_

_/...At least my math was right./_

_/You seem surprised, unusually so for an AI?/_

_/Is that what you think I am? An artificial intelligence? I can guarantee you that when this terminal was created, no man was capable of creating an AI./_

Doubt didn’t often plague Jim, but right now it was starting to niggle away like a bug in his brain, causing him to frown. Any kind of artificial intelligence created with modern technology wouldn’t be even half as self aware, but maybe… maybe it could be if there was enough time to evolve and learn. Time, like more than two hundred years worth. But a programmed AI is only as adaptive as its ability to learn, and with this old of a computer being a closed system, what could it have possibly learned?

Spock arrived then and Jim wasted no time in filling him in, and he agreed with Jim’s assessment, but still, that seed of doubt had been planted and it left Jim feeling a little off kilter.

_/How can you be so sure? Technology has come a long way since the 20th century; it wouldn’t be presumptuous to believe that a precursor to AI was invented even back then./_

_/...I think I’m missing out on some history. Can you give me an overview of the last two hundred and fifty years?/_

_/Only if you answer my question first: Who are you?/_

_/I can’t, not yet. There were very dangerous reasons for me to be here like this. People died, so I need to know if it’s safe./_

“Fascinating,” Spock said lightly, peering at the screen with interest. “This AI is unusually human in it’s self regard, with plenty of emotional sentiment for a program.”

“Yeah, ‘unusual’ is the word for it. I don’t know, Spock; something feels off,” Jim sighed, leaning back in his chair as he stared down at the screen. “If I didn’t know any better, I’d swear I was talking to a living person, not a program, AI or otherwise.”

“I can see how you have come to such a conclusion. Perhaps a ‘watered down’ version of history would satisfy its curiosity?”

“Yeah, I was thinking the same thing. Here goes nothing, I guess.”

_/Please keep in perspective that a lot of records were lost over the years, so there’s not a lot of accuracy./_

_/Fair enough./_

_/In between the years 2020 and 2053, there were two massive wars, the Eugenics Wars and World War 3; we don’t have exact start dates, but WW3 ended in 2053, leaving much of the planet devastated from nuclear warfare, and we don’t have almost any information from those years, or even of many of the years before 2020. The world started to recover from the nuclear fallout in 2079 and is now clean./_

_/That’s really depressing. It was always theorised that the next world war would be nuclear; guess it was right after all./_

_/First Contact with alien life outside the solar system was made in 2063 when Zefram Cochrane attracted the attention of nearby Vulcans passing through with the first human warp flight with his ship. There is now an interstellar government called the United Federation of Planets, made up of over a hundred planets. It's based on the principles of universal liberty, rights and equality, and it is the goal of the Federation to share both knowledge and resources in peaceful cooperation, scientific development, space exploration and mutual defence./_

_/...So there’s a governmental military?/_

“Based on the response, it would appear that the previously mentioned ‘danger’ was from the time period’s governing body. Concerns for safety seem well founded, if such truly was the case.” Spock summarised Jim’s increasingly discordant thoughts perfectly.

_/To a degree, yes. The Federation may be the largest governing body in the galaxy, but that doesn’t mean other species don’t want to conquer **us**. There’s a rampant slave trade in the more violent sectors of known space, for one, and at least half a dozen species that are not in the Federation are incredibly warlike. The Federation does defend itself, and those planets and species under its collective care. _

_Although I have to say that the reaction to alien life was a little… underwhelming?/_

_/That would be because my father, Kevin Flynn, discovered alien life inside a computer. I’ve been living inside the computer, inside the Grid this whole time. My name is Sam Flynn./_

“No way. No, that’s bullshit.” Kirk turned from the screen to stare at Spock incredulously. It mollified him to see the Vulcan also showing signs of disbelief, if minutely. “There’s no way this is possible, right Spock?”

“It does seem highly improbable, I agree.” One of Spock’s slanted eyebrows rose in a speculative manner. “However, it is not to say that idea does not have any merit; more information would be required.”

_/Forgive me if skeptical. Claims like that are… unusual, to say the least./_

_/You don’t believe me./_

_/Would you, if our positions were reversed? Like I said, most of the records were lost, either from the wars themselves or more corporate espionage or sabotage. What little evidence I have been able to dig up, almost literally, suggests that the Flynns were killed. After more than two hundred years, how can you prove that you are Sam Flynn and not an advanced Artificial Intelligence built and designed to his likeness?/_

The screen of the terminal sat silently as no reply came through. Spock, leaning almost casually against the wall next to the terminal, steepled his hands together in a motion that Kirk recognized as being meditative. Jim leaned back in his chair, running a hand through his hair with an explosive sigh.

This was big, bigger than anything Jim could have anticipated when he stumbled across that old ruin of an arcade. His research had shown him that the Flynns, both father and son, had been leading executives of Encom, back in the 1980s and in the 2010s, respectively. Both men had revolutionized the scientific world during those times before they both mysteriously vanished without a trace.

The implication of a hidden world inside a computer was staggering. What would it look like? How did it work?

Was it dangerous?

This was beyond anything Jim could have ever imagined.

The terminal pinged; new message received. _/What about a video call? If you could see me, would you believe me then?/_

_/Yeah, it would. At least, to start./_

_/Then what you need to do is fashion some sort of camera and hook it up to the terminal. The hardware that houses the Grid is incredibly advanced, way ahead of its time, but I figure that tech from the 23rd century would be easier to adapt to a pre-existing system. From there, I can manipulate the video output from your camera on my end and build myself a camera and connect the data streams./_

_/How is that possible?/_

_/Being a User has its advantages, but I can’t accurately explain it without you seeing it in person./_

_/User?/_

_/It’s what we’re called in here, those of us from the outside. Anyway, how long do you think it’ll take for you to build a camera?/_

“What do you think, Spock? It shouldn’t take Scotty longer than a week, right?”

“If that long. Mister Scott should be able to fashion a usable device within three days. It would also provide you with ample enough time to inform Admiral Pike. He may wish to be here for the video call.”

_/Give us three days. Shouldn’t take much longer than that./_

_/See you then./_

* * *

Three days later, Jim’s personal quarters on board the Enterprise were a little more crowded than usual as Scotty installed the newly built camera to the terminal, attaching a two foot wide monitor to the wall. The Chief Engineer had deliberately made the camera software plug-n-play, to be as non-intrusive as possible for the system they were syncing to.

Pike had joined them, along with McCoy who was currently giving the Admiral a minor check up while he could. Pike was confined to an experimental antigravity wheelchair, and it was unfortunately that he was likely never to walk again, but that was better than the alternative of death.

Minutes after Scotty had been finished messing around with the camera and turned it on, showing a small video feed of Jim in the top right corner of the monitor, the terminal gave a loud bell-like ping and the monitor blinked on and then there was a handsome face watching them sternly.

Jim blinked in surprise as the face staring back at them was a younger version of the corpse sitting in their Medbay, although there was an angry looking scar on his face that didn’t look exactly ‘normal’, but Jim would be hard pressed to answer why. The crystal-clear video feed allowed for most of the upper body to be visible, so Jim was able to scan the sleek black armour the man wore, but there small glowing white-blue lines in strategic places on his chest. The gray eyes almost seem to glow, and Jim felt that he was being judged and was somehow found lacking under that intense stare that could put Spock to shame.

What he could see of the room was confusing; dark walls in a material he’d never seen, bright lights coming from symmetrical patterns from the walls themselves, and maybe a couple of holographic displays, although from here, he couldn’t make sense of it.

“Sam,” The man said briskly, glancing off screen for just a moment. “It’s online.”

A second young man, about the same age as Jim if he had to guess, came into view of the feed, revealing a lean body and a tired smile to match tired blue eyes under messy blond hair. He was dressed similarly to the first man, entirely in black and armoured, but the glowing lines (white) were patterned differently, and to Jim’s keen eye, some of that armour looked reinforced.

“Thanks, Tron. Can you get a message out to the Sirens in the other sectors? I want as much of the City on lockdown as possible, just for the time being. I want Gemini close to home, too.” The young man sounded exhausted.

“Of course, Sam. I’ll be back soon.”

Then the other man was gone, leaving Jim and company to stare in silence as the young man smiled after his companion before turning his attention to the waiting video feed.

“Do you believe me now?”

Jim nodded, swallowing stiffly. “Kinda thinking that I have to, but yeah, I do.”

“So, you have a lot more people on your side than I do on mine; how about some introductions?”

“Sure thing. Ok, so that over there behind us is Chief Engineer Scott (call him Scotty), he was the one to make this vidcall possible; next to him in the chair is Admiral Christopher Pike of Starfleet, which operates the deep space exploratory and defensive services of the Federation; the one scowling next to him is the CMO of the starship Enterprise, Doctor Leonard ‘Bones’ McCoy,” Jim couldn’t help but grin as Bones slapped him upside the back of his head, prompting a startled laugh from Sam on the screen. “The serious one next to me is Commander Spock, First Officer of the Enterprise, and then there’s me; I am Captain James T. Kirk of the starship Enterprise.”

Sam watched them all intently, skepticism and doubt clear on his face. “So you’re all part of this… peaceful Federation of Planets? And your government won’t just.. Swoop in and kill us all for what the Grid can give?”

“Absolutely not,” Pike answered. “Any scientific knowledge has to be freely given and studied before all else. If you don't feel like your technology would be used appropriately for the benefit of Starfleet or the Federation, you don't have to share it."

This seemed to placate Sam, as his posture relaxed a bit. "That can work, for now. I honestly don't know. We were… we were doing a lot for the advancement of the human race, back in the 21st century, and I lost almost everything. I'm sure there's a lot I need to learn before I can even think about what the Grid can offer."

“That’s fair; you’ll have plenty of time to think about your options.” Jim reassured. “Now, who was that with you?”

Sam gave them a fey sort of smile. “Oh, I forgot. That was Tron; he’s a security watchdog program. I would have died in here long ago without him.”

“I’m sorry, did you just say ‘program’?”

“Yeah. Turns out that programs are like people in their own right, with feelings and thoughts of their own. Personalized programs like Tron look like their Users, but most of them are just as varied as humans.” Sam’s smile turned soft and full of wonder. “It’s absolutely unbelievable and amazing, the world down here.”

“Sam,” The other man from before - Tron, the _program_ \- stepped back into view, a gloved hand settling comfortably on Sam’s shoulder, handed the young man a drink, the liquid inside a bright fluorescent green. “You’re exhausted, Sam. Here.”

The light in Sam’s eyes as he regarded Tron told Jim that he absolutely adored the program, and wasn’t that something new? “Thanks, Tron. Mmm, strawberries this time.”

“Gemini is experimenting more; at this point, he could open a bar.”

“Maybe after we’re done with the restoration of the system.” Sam sipped at his drink (what was it?) as he turned his attention back to his waiting audience. “Did you have any specific questions?”

“Yeah, I got one,” Bones said gruffly, leaning down over the top of Jim’s shoulder to peer intently into the camera. “How in the hell have you survived for two hundred and fifty years?”

“Time works… a little differently down here, and the laws of time and physics don’t exactly apply here, either,” Sam’s expression took on a thoughtful look as he searched for the right words to explain. “You may have noticed that the terminal’s processing speeds have been slowed significantly; that was done on purpose.”

“Why was that?”

“Because without any tampering or tinkering, time moves so much faster in here than in the outside world; minutes up there would be hours in here. I don’t know the exact science of it, or why it happens that way, but my father, Kevin Flynn, ended up trapped in here for twenty two years on the outside…he lived for a thousand years here, and looked like he only aged fifteen years at the most.

“So, because I couldn’t be sure how long I'd be in here before being discovered and couldn’t even fathom the idea of spending the equivalent of millenia down here without losing my mind, I changed the core programming and reversed the time dilation. Now, for every thirty minutes in here, about a day passes out there. The only reason we’re able to speak is because of a communications program I was writing for NASA, using quantum physics and mechanics, and a customized quantum entanglement relay." Sam said with a small flourishing wave of his hand, and behind him, Tron looked almost proud.

Jim glanced around to gauge the reaction of the others, finding them notably impressed. "That's what… three years, give or take a month or two?"

Sam nodded, setting aside his empty glass. "Yeah, basically. So I'm not exactly sure I can die in here; of old age, at any rate. Down here, I don't need food or water to survive, but I can still get hurt and die that way."

"Kid," McCoy's tone was as serious as it had ever been, intense and highly focused. "How hurt are you, right now? And don't sugarcoat it, either."

"I'm as alright as I can be, without proper medical attention, but…" Sam sagged in his seat, shoulders slumping like a puppet with its strings cut. "I don't know how much longer I can keep this up. My dad made it as long as he did by hiding in the Outlands for a thousand years; I've been working to restore what's been broken down here."

"Users are incredibly powerful," Tron interjected, running his hand down Sam's in a comforting gesture. "But they are not infallible, and we are not equipped to adequately care for Sam's health."

The security program then outlined Sam's injuries from the past three years, while Sam interjected that he hadn't been at peak capacity before hiding inside the Grid, which didn't help. McCoy had been suitably horrified and he and Scotty, with Pike's official permission of course, had started devising a way to at least send some equipment down into the computer.

Sam told them that he could build anything on his end, so long as he had an understanding of the technology and it was Spock who had the idea of downloading blueprints for the medical equipment directly into the terminal.

They agreed on medical scanners, to at least give them an accurate assessment of Sam's health and wellbeing, and depending on the results, would decide the next course of action.

Since Sam was no doctor, and depending on the results from his impending medical scans, McCoy wanted to somehow travel to the Grid or bring Sam out, at which point the blond on the other side of the screen pointed out that the Grid was like a safe: could only be opened from the outside. Someone was going to have to go into the Grid, and from there, Sam could bring them out again.

Scotty started scrambling to try and maybe improvise with the transporter pad settings when Sam cut in asking about the laser that would have been found in the same room as the terminal, revealing that the laser was in actually almost a precursor to Starfleet’s transporter technology, only instead of converting matter into energy to be sent to another location and reconverted, the digitization laser converted matter into digital code. From there, Spock speculated that perhaps the reason that Sam didn’t require normal human needs to survive was because he was very loosely, and maybe only ’technically’ a digital construct in his current location.

After thinking about it for a few minutes, Sam agreed with Spock, with an added amendment that it could be quite the philosophical debate.

In the end, the plan was that McCoy and Spock were going to collect and download a couple of medical blueprints for Sam while Scotty and Kirk prepped the laser for use. By the end of a week topside (so to speak), they would send McCoy down into the Grid and bring Sam up and into his Medbay for treatment. Pike also reminded them that the Enterprise was due to ship out in five weeks and there was still a lot of work to be done by all members of the senior officers, but that he would be more than happy to provide Sam with a Federation identity (and Tron, as the program boldly stated that he would not be leaving Sam’s side for any reason) and temporary Starfleet credentials to allow them to be a part of the crew, even if only on a technicality.

The Admiral did mention that they were more than welcome to apply for those credentials for real, should they want to.

Before Kirk disconnected the call, McCoy had one last question for Sam. “You gonna be alright, kid?”

Sam’s answering grin was a little rueful. “Yeah, I’ll be fine. I’ve been dealing with these injuries for two years now; four or five hours will be no problem. Tron can keep me safe for that long. We’ll be waiting for you.”

“See you soon, kid.”

**Notes for the Chapter:**

> I did struggle a bit with this one, technical stuff mostly. I got most of it figured out, but please let me know if there any glaring errors.
> 
> I also hope to keep rough schedule of updating mostly once every 1-2 weeks, but I cannot guarantee it, as we are starting to go into unknown territory.


	7. Chapter 7

"Bones, you'll be fine; nothing's gonna go wrong."

"And how in the hell do ya know that, Jim? You're not the one getting transported into a goddamn computer! This is _beyond_ any of the weird shit we’ve done before!” Bones broke off before his anxiety could truly take over, raising one hand to pinch at the space between his eyes, feeling a headache coming in. “Look, kid, I know I’ll be fine. I’ve got bigger priorities to worry about.”

Jim Kirk watched from across the small room as his closest friend paced furiously, anxiety fairly rippling through the air. Bones had never enjoyed the transporter pads on board the Enterprise, even as advanced as it was, which made the notion of being digitized a particular harrowing idea that only truly set off Bones’ nerves in the last twenty four hours.

Kirk had decided to keep the digitization laser in the otherwise empty engineering lab, hooked up to the ship’s systems and connected to the computer terminal still in his quarters (although that was likely to change in the next couple of weeks) and connected to the laser through a modified wireless transponder. The lab was also going to be sealed off from the majority of the main crew; only specific individuals would have access and would require at least two people to be in the room. There would be no one allowed alone, in order to maintain secrecy and to prevent accidents.

Although there was, already, some general curiosity from the rest of the crew as they scuttled about doing all manner of systems checks, last minute ship diagnostics, and general restocking and long term inventory checks in preparation of their upcoming five year mission.

The Enterprise crew was wickedly sharp and discrete, a point for their valor in Kirk’s book.

The ship’s intercom pinged, drawing the attention of both men. “Captain, we are ten minutes out from the appointed hour; you are needed at the terminal for the initial countdown. Doctor, how are you faring?”

“I’m fine, thank you, Spock. Just getting over some last minute nerves, is all.” Bones seemed to calm, his demeanor hardening into the no-nonsense Starfleet Officer that he was. “You better get going, Jim.”

Kirk nodded, already walking for the door. “I’m on my way. You sure you’re alright, Bones?”

“Yeah, get goin’.” Bones waved him off, moving to stand in the marked space in front of the laser, folding his arms under his chest as he did so. He waited in place, focussing on his breathing to calm his nerves until the intercom pinged a second time, and he breathed in a deep fortifying breath of air.

“Ok, Bones: T-minus fifteen seconds. All you’re doing is grabbing the kid and getting out.”

“I know, wish me luck. I think he’s about as stubborn as you are.” He ignored the way the laser powered up, the tip of the machine pointed directly at his chest.

Kirk laughed, the sound just the smallest bit tinny. “Good, I like that. Five, four, three, two, one.”

There was a blinding flash of light and McCoy’s heart lurched in his chest. He stumbled in place, opening eyes he hadn’t realized he’d closed when the laser beam hit him. A look around the dark room told him that he was no longer on board the Enterprise, at least not in the technical sense.

He took a few unsteady steps forward, expecting some company for his arrival, and was a little disappointed (and annoyed) that neither Sam Flynn or Tron were there waiting for him; that was the whole point of this little excursion.

Instead, just beyond the small room he arrived in, someone else was waiting for him, and the man looked like a lot like Sam, like he could pass as the kid’s brother. The shape of the face was the same, but McCoy thought he could be taller, maybe a little wider in the breadth of his shoulders, and the eyes were a dark sapphire blue, a literal spark faintly visible. This man wasn’t blond like Sam either, instead his hair was almost black.

“You the welcoming committee?” he asked a little gruffly, irritated that his potential patient was nowhere close by.

“Yes, my name is Gemini, a systems utility and administrations program, and I am at your disposal for the duration of your visit.” His voice was rough like Sam’s but the inflection was more like Spock’s to McCoy’s ears. “I apologize for SamFlynn’s absence, but there was an incident in another sector of the city that required the attention of a User, and of course, Tron went with him.”

“Is everything all right? The name’s McCoy, by the way.”

Gemini ushered McCoy away from the portal room, one hand barely touching the doctor’s lower back as he led the User into the armory. “While we have regained control over most of the city, there are still a few sectors with distinctive hostile tendencies towards Users, and our allies in some of the neighboring sectors were concerned that their defences would not be enough during the current lockdown.”

“And Flynn is the only one who can really do anything about it?”

“On a larger scale as needed, yes. Users are incredibly powerful and unmatched in their abilities, but SamFlynn’s learning curve was… steep. Thus the reason why you are here.” Gemini tapped once on a brightly lit node on the wall, raising a small platform from the floor. He gestured for McCoy to approach the platform. “Please step up here. Your current attire will not only attract unnecessary attention, but will leave you entirely defenceless. You will also need to be fitted with an Identity Disk.”

“Will I still have my clothes when I leave?” McCoy asked as he stepped onto the platform, feeling a little trepidation, unsure as to what, specifically, was going to happen. The last thing he wanted was to lose his clothes; Jim would never let him live it down.

“According to my User, yes, you should have everything in original condition once you go back through the portal.” Gemini disappeared behind him and he felt the lightest of touches running up his arms from the wrists to the shoulders then down his back and down each leg, the faint touch warm against his skin, economical in the movement but oddly… sensual.

Then his clothes fell to the gleaming floor, leaving him in his Starfleet regulation black briefs (even his boots were destroyed), and the remains of his uniform were sucked away beneath the platform.

“Gotta admit; feelin’ more than a little exposed here,” he said rather glibly, smirking as Gemini snickered from where he knelt at his feet. The program tapped a couple of keys and a curious black synthetic material crawled up his limbs, outfitting him in a form fitting black jumpsuit that covered every inch of skin from his toes to the first half inch of his neck, including most of his hands, leaving his thumbs, pointer and middle fingers bare. “So what’s this about a disk?”

“Your Identity Disk is everything; everything that you are, and everything that you learn or do will be imprinted onto your Disk,” Gemini walked over to one of the walls, pulling down different of what could be armour and bringing them over to a small table that was strangely floating in midair. Setting the pieces down, the program started to attach them at certain points, fitting them to the contours of his body; knee pads, a belt around his hips, simple gauntlets to his forearms, a shoulder pauldron on the right side and a small chest piece. Once in place, the separate pieces lit up in symmetrical lines of a gentle lime green, additional material forming in place to connect most of the pieces into a singular cohesive piece protecting most of his vital organs without impeding his range of motion.

“Fascinating; this is a rare color. Most programs with this color have it as a secondary function on smaller nodes.” Gemini traced a finger down a pair of circuit lines on McCoy’s left arm, right below an arm band that held a glowing version of his Starfleet emblem in sapphire blue with the medical cross glowing a bright red. The touch sent tingling static up his spine. “SamFlynn said you’re a doctor; what exactly does that mean?”

“Being a doctor means I fix people, that I heal them,” McCoy said, watching as Gemini pulled out a black ring about the size of an old fashioned frisbee from a small panel in the wall that vanished as the program walked back over to him. “I’m not really sure how that translates for programs, but maybe… an antivirus?”

“Repairing programs just sounds like what Users are reported to be able to do as a given, but being an antivirus sounds accurate.” The program stepped neatly behind him, securing the ring to the armour covering his back. A sharp click sounded and McCoy’s vision sparked. “Identity disk has been synced and activated.”

“So what now? How long do you think the kid will out for?” McCoy asked as he stepped off the platform, intrigued at his new gear as he followed Gemini up the stairs to the main floor of the nondescript building they were in. All the materials were dark and smooth, not at all like old brick or concrete or even the durasteel plating used in building starships; instead the material was smooth like glass, completely opaque and covered in faint geometric designs. Bright lights came from nowhere and everywhere, and holographic displays floated freeform throughout the open space.

McCoy was drawn to an impressively detailed and complicated holomap of what looked like a large city, color coded into different sections. Most of the sections were lit up in blue or yellow, but a few were lit up in red. One sector in particular, Sigma Sector, was highlighted, showing a multitude of tiny blips that the Doctor could only interpret as the disturbance Gemini had mentioned earlier.

“Tron mentioned that they should be back within an hour or so, but in the meantime, I was supposed to show you the results from SamFlynn’s medical scans,” The utility program walked over to a table off to the right of the map, swiping at the air and bringing up floating diagrams, including a full body scan that showed a few problem areas that McCoy would have to investigate further. “Your blueprints were followed to exact specifications, as you can see. I’ll be honest; it’s distressing to see that Users are so… vulnerable. And yet they are so resilient. I have seen programs take less damage and succumb to deresolution, but on the other hand, any damage sustained can be repaired so much easier.”

Gemini showed the doctor how to use the interactive interface of the floating diagrams, which he found to be surprisingly intuitive, before leaving the User to go over the reports on the holographic screens.

McCoy’s mood dropped as he first looked over the rudimentary x-ray scans that told him all about the various serious injuries his soon-to-be patient had incurred over the past couple of years. It was increasingly obvious that medical supplies were practically nonexistent beyond whatever Sam had created (manifested? He wasn’t exactly sure yet), but those measures were more of a stopgap measure, a metaphorical bandaid. The newer scans from the equipment he’d had downloaded into the system told him that Sam’s body was suffering from prolonged pain that went untreated for the most part, and the resulting physiological and psychological damage incurred from prolonged and untreated pain management was starting to take its toll. He also noted signs of anemia, as there had been at least once incident of massive blood loss that also wasn’t treated correctly.

Sam was going to need surgery to repair some of the leftover damage of wounds and bone breaks that hadn’t quite healed right (and were already showing signs of additional stress fractures, further compounding the issue); his largest concerns being the most recent collarbone break (the broken pieces weren’t aligned properly) and the older leg break, which he suspected had progressed into a bit of a limp.

McCoy had already started planning out a treatment regimen when an alarm blared throughout the building, sounding as loud as an airhorn. He spun around, looking for Gemini as several of the bright white lights turned an angry red; the utility program bolted from the basement with one hand pressed to the side of his visor by his ear. His expression went from worried to panicked in a second and he bolted out the door leading outside. McCoy followed after him, momentarily distracted by the shining brightly lit skyscrapers under a rolling sky that raged in a never ending storm.

“Doctor! There’s an emergency!” Gemini’s voice rang out from across the open and wide street, drawing McCoy’s attention from the starkly beautiful skyline to a massive ATV type vehicle skidding to a halt right in front of him, the passenger side door swinging up and open. Gemini waved him in frantically, fear bright in his eyes.

“Get in! They were ambushed and Sam’s been hurt!”

“How far are they?!” McCoy jumped into the ATV, the vehicle speeding away before he was even settled in, but after so many disastrous away missions with Jim Kirk, McCoy was used to out of control scenarios. “What can you tell me?”

“We’re twenty minutes out and several of our allies from neighboring sectors are already there to help secure the situation,” Gemini’s grip on the steering wheel was clenched tight, eyes unwavering from the road. “The city’s been on lockdown since your first message, and security has been increased since the portal opened with your arrival.”

“Why are there tensions anyway?”

“This goes back a long time, but when Kevin Flynn created the Grid, he created a program to help him, called him CLU. Flynn, CLU and Tron were here from the inception of the Grid; Flynn to create, be the User, Tron to protect the system, and CLU to help run it.” Gemini glanced over at him in the passenger seat. “The goal was to create the perfect system, but somewhere along the way after the discovery of the ISOs, CLU became corrupted. He felt that these spontaneous programs were flawed, an imperfection, even as Flynn saw them as a miracle. CLU purged them all and while there was one survivor, he spent the next thousand years building an army with which he was going to use SamFlynn or someone else from the outside to reopen the portal to invade the User world to create the perfect system, and to quote Kevin Flynn ‘the guy doesn’t dig imperfection, and what’s more imperfect than our world.’”

“And that army is still active, I take it?” McCoy threw an arm to the door to brace himself as Gemini turned a corner sharply enough to jostle him in his seat.

“The last remains of it, yes.” Gemini frowned hard, looking unsure of himself even as he pushed the ATV even faster. “Look, you’re a User and you have no idea what you’re capable of down here.”

“How do you mean?”

“Users are all-powerful creators, capable of building and creating what they want, when they want. I asked Sam about it once; he described it as a sense of perception. He stretched out his senses, and was able to… see? Feel?” The program shook his head in distraction. “He could directly access the code in the very air and he could manipulate it to do his bidding. Tron says that Users are only limited by their imagination.”

McCoy did not feel at all confident about where the program was going with his line of thinking, but he had been friends with Jim long enough to take an educated guess. “What are you thinking, Gemini? What’s the plan here?”

“We’re still ten minutes out, and we have no actual medical supplies because programs don’t need them like Users do; all repairs to our root code can be done through direct access to our disks; and Users don’t have root code like we do.” Gemini glanced at him, a pleading look lining his face. “I think we’re going to need you to make use of those gifts that make you a User. Look within yourself and try to sense the lines of code in the air around you.”

McCoy was skeptical, but he did as Gemini asked, looking deep within himself, chasing the feeling of calm he got and used when he was in the OR, for that was the time when he was at his very best; where he was in complete control of the world around him.

He stretched out his senses, closing his eyes as he did so, and after a few minutes, he thought he could maybe understand what Gemini was trying to teach him. The program was bright to his perception, and he could feel the walls of the ATV and the streets they were flying down, almost like echolocation. His fingers twitched at the sensations teasing his senses.

Noise up ahead brought him out of his trance-like state, and opening his eyes, McCoy could see a battlezone. The street was wide and clearly a border between two warring parties, although it was clear that the red lit programs were the aggressors, although they were all in the process of being contained. There was a red and orange colored substance like snow scattered in a lot of piles, and McCoy recalled that program-based death was called deresolution.

By the side of a towering skyscraper, a group of people were gathered and all of them were armed with their disks and energy swords lit up in varying shades of blue and red and locked in battle. McCoy could see that some of the blue programs were trying to guard something (someone) on the ground, and even from where he was in the ATV, he could see a disturbing amount of blood, the bright red contrasted sharply with the dark street.

Before Gemini could pull the vehicle to a stop, McCoy leapt from the ATV, dodging both debris and bodies while running for Tron who was kneeling next to a body that was far too still. “Out of the way!”

A hulking red program sneered at him, ugly and hateful, and leapt towards him, his disk vibrating violently and some instinct had McCoy dodging the blow and pulling his own disk free and throwing it. The attacking program shattered in front of his eyes like a wall of tempered glass; the sound simultaneously delicate as silver bells and the grating screech of crushed steel.

The only reason that Sam was still alive was because Tron was keeping a firm unwavering pressure on the wound, a deep laceration high on his right flank, high enough that McCoy was worried about his lungs, and certainly his liver was already perforated if not torn in half from the depth of the laceration. “Where else is he hurt?”

“Most of the renegades were already contained, but I was already fighting four of them so I couldn’t get there when one took him out at the knee. He couldn’t move, at all.” Tron spoke quickly, fear and worry thick in his voice. He looked wrong, out of place with his hands covered in Sam’s blood, but he didn’t move them, keeping as much of Sam’s blood _inside_ his body as he could.

“Do what you need to do with regards to security and the rest of the renegades. Keep everyone else off my back,” McCoy shooed away the security program, easing bloodsoaked hands away from the grievous wound, seeking that level of zen-like perception he had found on the way here, seeking that sense of cool calm he used in surgery. Following instincts he didn’t know he had, McCoy pressed a hand to the wall of the building, the wall sliding a panel open to reveal freshly constructed equipment. A visor materialized over his eyes, armour plating caressing the back of his skull, the clear glass of the visor giving him active real time diagnostics of Sam’s condition. “Gemini! Get over here!”

McCoy attached bits of manifested machinery to various parts of Sam’s body, not even phased as they expanded seamlessly to suit his needs (and were transparent), holographic readouts showing him everything he needed to know. Not only was Sam’s left knee was completely shattered and would complete reconstructive surgery, the younger man needed immediate triage to at least put a bandaid on the laceration that threatened a bleed out if he didn’t hurry; his only saving grace was that wound was cauterized, effectively minimizing the loss of blood and likely caused by a thrown disk.

Sam’s lung had been nicked by the enemy disk, so that was McCoy’s first concern. He directed Gemini on stabilizing Sam’s shattered knee; how to operate the equipment he created to start the process that he would be able to finish in his Medbay. They only needed to stabilize Sam long enough for travel back to the portal.

Focusing his attention on the field surgery, McCoy’s hands started glowing in tiny precise lines of a vibrant green, his fingertips turned into scalpels and medical lasers as he needed. He cut and welded muscle and tendons back together with precise, neat movements, near oblivious to everything around him beyond the circle of programs guarding them from sight. With his increased perception, McCoy could feel the code flare up around his hands as he dug into Sam’s side, repairing what damage he could without being in a fully equipped OR.

Finally, Sam was in a stable condition, his side held together with manifested bandages and his knee splinted in a makeshift cast to keep it locked in place, although he was still deeply unconscious. McCoy felt he was ready to be moved, but his pallor was too weak. “Gemini: do we have any sort of painkillers?”

“Here, liquid energy,” the program next to him handed over a crystalline flask filled with a curious brightly fluorescent yellow liquid. “This is as close as I’ve been able to make. It’s dulled his pain before, and seems to act as a kind of blood replenisher.”

“Good enough. Here, help me get him to drink it.” He directed the program to prop Sam up carefully, just his shoulders and head while he tipped the flask to pour the energy drink down Sam’s lax throat, massaging the muscles there to induce swallowing. There was an almost immediate effect of some color returning to Sam’s face.

“We need medical evac, now. This is just a stopgap measure.” McCoy sealed the flask and placed a bloodied hand to the street beneath him, constructing a stretcher for Sam in the matter of a few moments. He helped Gemini move Sam over onto the stretcher and with the help of Tron, loaded the stretcher into the back of the ATV (no, down in here it was called a Light Runner) and soon after, the four of them were speeding off back to base. Sam was stabilized for the time being, but McCoy wasn't sure how they were going to get the kid out. “How do we use the portal to get back to the outside?”

Tron was driving them back, hands tight on the wheel, speeding through the streets with an urgency that McCoy was sure was directly related to how he felt about the injured young man. “I’ll need Sam’s disk, but I’ll take care of it; you just make sure he survives this.”

“Like that was ever in question, kid.”

The rest of the trip was a bit of a blur for McCoy, but back at the arcade, Tron grabbed Sam’s disk, which was explained as being the new Master Disk, and hurried ahead of him and Gemini to prepare the portal for the return trip home. Gemini, with his superior strength, helped McCoy carry Sam down into the basement while McCoy used his still glowing hands as a kind of medical tricorder, a small display hovering above his left wrist. He wanted to know the second Sam’s vitals dropped, but he was confident they could make it until they were topside.

Tron alerted them that the portal was ready for them, that all they needed to do was step inside the tiny room, so the security program gently gathered Sam carefully in his arms and handed McCoy Sam’s disk reverently, treating the circular object much like a holy relic. McCoy came to the startling realization that, in a way, maybe it was. “All you need to do now is raise it above your head, keeping the ring flat. The portal will take care of the rest.”

“Got it,” McCoy nodded sharply and turned to look over at Gemini, where the program was watching them from the doorway, looking like a frightened calf. “You did good, kid; I’d be more than happy to have you as a nurse any day.”

Gemini smiled weakly at that, never taking his eyes off Sam. “Thank you. Please -! He’s… he’s my Creator.”

“I’ll send you a message when he’s out of surgery, ok kid? He’s gonna be fine.” McCoy raised Sam’s disk above his head, freezing as the disk got caught in the growing beam of light until he couldn’t see a thing.

There was a flash like a supernova igniting and McCoy found himself back on the Enterprise, with Tron and Sam at his side, the program carrying the wounded man. The CMO lept into action, calling for his Medbay to prepare for surgery and requesting a stretcher to meet them enroute. Jim and Spock were there, too, wanting to know what was happening, but McCoy ignored them as he ran into his surgical team and loaded Sam for the Medbay shouting orders to his staff as he went.

A look to Tron showed that the program was trailing after him, but McCoy couldn’t allow him into the OR. “Tron, I’ve got Sam. Report to Jim Kirk and I’ll report back to you as soon as I can!”

The security program hesitated only minutely, desperately wanting to stay at his User’s side, but he could see the logc to McCoy’s orders; he would only be in the way. “Understood.”

Tron didn’t follow as McCoy vanished into Sickbay with Sam and his team, the sudden silence of the hallway jarring as the door slid shut behind the doctor.

* * *

"Hey, let's get you cleaned up." A familiar voice to his left, and a light touch to his elbow drew Tron's attention from the closed doors of the Medbay. Tearing his eyes away from those doors was an almost insurmountable task but Tron forced himself to regard James Kirk with distracted intent.

The young man looked so much like Sam that Tron’s chest hurt, like a vice squeezing the air from his lungs, and some of that must have been obvious because Kirk grimaced and started leading the program away from the Infirmary with a careful grip on his arm. The halls were busy, filled with people dressed in uniforms that only varied in color (blue red gold), and all of them, while remaining professional, were giving Tron looks of concern, curiosity and wariness.

He realized that he was covered in blood (Sam’s blood) and the air rattled in his lungs as his world narrowed to the bright red color staining his fingers. Sam had been hurt before, but not like this, and his ears rang with the memory of Sam’s agonized scream as the disk serrated through his flesh with an ease that chilled Tron to the core of his programming.

Tron blinked to block away the memories and found himself in another location, that Kirk had moved them along without his knowledge, but the sense of familiarity he shared with Sam banked the growing sense of unease, and he tried to focus on his surroundings. He focussed on little things first, like his clothes; Tron was no longer wearing his signature armour but instead was clothed in dark jeans like he had that night oh so long ago when CLU had initiated his coup, the dark leather of his jacket at once familiar and alien on his skin.

His location was more isolated, out and away from the busy corridors, with only two other Users aside from Kirk, but he ignored them as he noticed a large window along the far wall, a strange and alien (wondrous) sight drawing him closer. On the other side of the window lay a vastness of black emptiness the likes of which had never seen, could never have imagined. The construct they were in (the starship maybe?) floated in a shipyard of sorts, hanging over the curvature of an immense blue sphere, the sight of which filled Tron with an obscure sense of melancholy and longing, one he couldn’t place the reason for. Looking back out into the inky black, his keen eyesight picked out millions upon million of twinkling lights, like distant portal stars.

It made him feel so very small.

It was also so heartbreakingly beautiful and stunning in its scope and Tron desperately wished that Sam was right here to show him everything about his world.

“Tron?” A soft voice, female, cut through the fog in his head and it took more willpower than he was willing to admit to tear his gaze away from the view and look to the Users in the room. Kirk was gone, but in his place stood the woman, tall with dark skin and long dark hair, clad in red, beautiful and cunning. Next to her, a man in gold and black, black hair and slanted eyes watched him with concerned curiosity. “My name is Nyota Uhura, and this is Hikaru Sulu. Kirk had to go but he asked us to take care of you until he gets back. Is that alright with you?”

“What do I need to do?”

"I'll get some clothes for you," Uhura said gently, voice low and tone soft. “Hikaru is going to help you clean this blood off. We’ll make sure that your clothes get cleaned, too.”

Tron’s brow furrowed in confusion, even as he followed the two Users through a door to a smaller room that contained a row of sinks and shower stalls. “But- I was supposed to debrief with Kirk? McCoy ordered me to see Kirk.”

“We’ll take you to him after we’re done here,” Sulu countered, and to Tron’s keen eyes, he was confident in his abilities and himself, which calmed Tron’s scattered nerves. “Kirk needs to find Admiral Pike anyway, from what he said.”

The woman (her name was Uhura) vanished with an economical flip of her long hair, disappearing to her self appointed task while Sulu leaned Tron’s back to the wall next to one of the sinks and turned the knob, releasing a stream of water into the basin. Tron only knew it was water because Sam had told him about the substance once - as life giving and essential for the survival of Users as energy pools were rejuvenating to programs. Sulu helped him out of his jacket and tshirt when his limbs failed to cooperate and started washing away at his hands, gently cleaning the blood away from his skin with firm, even passes of the rag he produced from somewhere; it was difficult for Tron to pay attention.

"So Kirk gave us the bare bones of the situation; a secret mission, things obviously went wrong, and also that you're not exactly human. So, I gotta ask; what's your story?" The User kept his voice calm and even, non threatening as he went about his task and Tron drew strength from that chill efficiency, finding it familiar.

"That would be correct: this world is so alien to me." Tron's breath came in shuddering gasps as he longed for Sam; his codependency for his User, his partner, was shocking to him. And yet, not surprising at all as he could fully admit to himself that Sam was practically embedded into his root code. "I am a security firewall and watchdog program, a digital construct of code, and Sam is a User; the closest equivalent to what he called a diety. You, too, are a User, to put it in perspective."

"And what happened?"

"Last minute disturbance before we were to leave, because Sam was already hurting. It should have been routine, an easy fix; but we were ambushed." The memories surged forward in his head, making his chest hurt like the night he failed Kevin in CLU’s coup. “Sam has worked too hard for some low-bit _renegades_ to take away his success.”

"And things went to hell."

"Exactly."

Uhura returned a few moments later, a black undershirt in her delicate hands. She helped him maneuver his stiff arms inside and pulled the fabric over his head while Sulu cleaned up and the two of them guided him through the corridors and up an elevator until their small group was ushered into a conference room, joining with several others. Tron recognized them all from the vidcall; Spock, standing tall with his hands clasped behind his back; Pike, still ensconced in his chair but clearly a leader, confident and calm; and Kirk, impatient and worried but carefully hiding it beneath a cool veneer. If Tron didn’t know Sam (and the masks he wears) so well, he wouldn’t have been able to read the young Captain so accurately.

Admiral Pike led the debrief,seating the party at the conference table and asking Tron for a clear accounting of events from the end of their vidcall, ignoring that Uhura and Sulu had taken point next to the program, just as he brought no attention to the fact that Uhura had taken one of his hands in hers, offering silent support.

He appreciated it, and he felt that Sam would adore her.

Mechanically, Tron led them through the chain of events of the past couple of hours (to him, he was vaguely aware that days had past for the Users) from the distress signal from one of the neighboring city sectors, to securing their allies from the Sirens running the neutral sectors, to engaging the hostile remnants of the Black Guard, to being ambushed and nearly overwhelmed, to being too occupied with his own fight to protect Sam, to that horrifying moment that Sam fell in a pool of his own blood and didn’t get back up, to the saving grace of McCoy and Gemini arriving on the scene and the doctor rushing to Sam’s side and the subsequent retreat back to the arcade and escape from the Grid through the portal.

At some point, a low ticking purr blurred in with his words, intense stress allowing that aspect of Rinzler to shine through. It garnered a few looks of concern, but it wasn’t commented on.

His words died out as he recalled how lifeless Sam had looked in those few moments before McCoy had sent him away. His vision blurred and he blinked and felt something fall down his face.

_Oh._

Tron was crying.

“I cannot lose Sam. I have already lost everything: my Creator-User, Alan-1; Sam’s father, Kevin; my own identity and purpose for a thousand years. Sam is all I have left.” Hr brought a hand to his face, wiping away the tears carelessly.

Pike was solemn as he watched the program seated across from him, noting how Sulu reached over and placed a comforting hand on Tron’s shoulder and how Uhura continued to hold his hand, stroking her thumb across his now clean knuckles. Looks like the senior staff of the Enterprise was already adopting their new civilian crewmates. “Please be assured, Doctor McCoy is one of Starfleet’s best surgeons. Mister Flynn is in very good hands, but I won’t lie to you; I’ve seen the preliminary reports of the young man’s injuries, and he’s in for a very long recovery.”

“I’ll do whatever I can to help. I fight for the Users, and he is my partner.”

“Right now, all you can do is wait; surgery is a long and complicated process, and Flynn’s injuries makes for a longer process.” Pike held up a hand to forestall Tron’s protests. “We’ve got a set of quarters for the two of you, so right now, we’ll get you settled in and the moment that Flynn is out of surgery and ready for visitors, you’ll be the first to know.”

“I need contact with the Grid. Sam’s program, Gemini, needs to know what’s going on, and I need to relay orders to keep operations running smoothly.” He felt better with a sense of purpose, although he was dreading the waiting.

Pike nodded, acquiescing to the request. “Of course, Captain Kirk will be more than happy to take you to talk to your people.”

The meeting concluded shortly after that, with Spock conferring with Pike in low tones that Tron ignored as unimportant in that moment as Kirk led the way to where they’d stashed the Grid terminal, Uhura and Sulu trailing after them like shadows. Kirk reassured Tron that McCoy would do everything in his not-insignificant power to help Sam, that the Doctor truly was one of the very best in his field.

Once inside Kirk’s personal quarters, Tron was able to get in contact with Gemini, reassuring the younger program that Sam was going to be fine and giving him orders to patrol the city for any further disturbances. It would give Gemini a sense of purpose until either McCoy or Sam sent word.

After the vidcall was finished, Kirk led Tron to where he and Sam would be lodged during their stay in the organic User world, while also promising to move the Grid terminal down from his quarters to these rooms as soon as was possible, and Tron was once again drawn to the large window, entranced by the vast blackness of space.

Uhura approached him with a small handheld tablet, much like the one Sam had made for him to use inside the Grid. “This PADD will allow you general access to information while you’re here. You’ve got a civilian login to the database libraries of the Federation, and if you have any questions, please feel free to ask. I’m hoping that this will help pass the time until McCoy gets out of surgery.”

Tron accepted the tablet from her hands, giving her a small smile for her forethought and generosity. “Thank you.”

Her own smile was sad as she wrapped her arms around him and pulled him close, embracing him with a warm hug that softened the pain in his heart. “Everything’s going to be just fine now, honey. It doesn’t matter what happens next, you and Sam, and whoever else from your world, you guys are a part of our family now.”

Tron returned the gesture, wrapping his arms around her slim waist while both Kirk and Sulu echoed her sentiments. He felt relieved to have gained such staunch allies in the short time he’d been here.

“Thank you all. Sam and I would be honoured to call you our family.”

**Notes for the Chapter:**

> There were a few places where I wasn't exactly confident in my portrayal of events. Like, how do you even describe the magnificence of seeing space and the earth for the first time as a program who doesn't even have the terminology?
> 
> I hope I did alright, but I am open to suggestions, too.


	8. Chapter 8

**Notes for the Chapter:**

> I've got to admit, but I struggled with this chapter, a lot. RL issues got in the way, too, so apologies for being late.

Sam came out of surgery ten hours after he went in, and while the surgery was a complete success, McCoy had restricted all access to him until he had woken up on his own, after the antibiotics had run through his system. He needed to rest, especially after the surgery and the round of modern vaccinations that Sam needed in order to remain living in this future world, which further drained his healing body of energy.

McCoy was only grateful that being turned into digital code hadn’t any long-lasting negative effects on the human body, like malnutrition or common illnesses, and only short term effects like acute exhaustion. The liquid energy that Gemini had provided took care of those bodily needs, it seemed, and McCoy would have given anything for a sample, but he realistically didn’t know if that was possible, since the energy came from a digital world in a state of matter that was different from energy out here in the organic world.

Tron had chafed -fiercely- at being denied access to Sam right away, but once McCoy explained the reasons behind his call (keeping the patient isolated to avoid possible infections, while finishing the first round of antibiotics, etc.), the program accepted it, if unhappily.

In the meantime, the security program had veritably attacked the Federation libraries, reading and assimilating vast quantities of information at a speed typically only achieved by computers, which made an unsettling amount of sense for those few crew members directly in the know of the secret that was Tron and Sam Flynn.

It was until almost three weeks after Sam and Tron were pulled from the Grid that some of the physiological differences between humans and programs became apparent when Pike received a notification of a systems breach in Starfleet Intelligence. The only reason SI hadn’t directly reacted to the breach was that nothing was being stolen or downloaded - only accessed. SI had also managed to track the source of the breach (although with some difficulty that clearly rankled the higher ups), and since it was coming from the still docked Enterprise (some mechanical concerns down in Engineering had delayed the starship’s departure), they were giving Pike the chance to find out what exactly was going on, especially since it was coming from a Pike-approved civilian account.

That told Pike exactly who was responsible for the breach, and was precisely the reason he found himself invited inside the civilian quarters assigned to young Mister Flynn, now on Medical Bedrest, and his program companion.

“Sir? What’s this about?” Sam asked from the bed, where his right leg (completely encased in a cast from knee to ankle, for both the recently shattered knee and the newly repaired shin injury) was suspended from a pulley system from the ceiling. His left arm was also in a cast from surgery to repair the incorrectly healed break there, and his torso was wrapped up tighter than an Egyptian mummy. Both casts also had Osteo-regenerators attached to promote the healthy healing of the damaged bones. McCoy had already given the kid a recovery period of six weeks, sooner if he was able to start with physical therapy ahead of schedule.

“I’ll get straight to the point: Tron, have you been accessing restricted files within the databases in Starfleet Intelligence?” Pike asked glibly, a diplomatic smile on his face giving nothing away to the other three people in the room; Spock had joined him in Kirk’s stead, the young Captain being trapped in meetings with the rest of the Brass to finalize a few things before the Enterprise could on its five year mission in just over a week (barring any more delays).

Sam’s jaw actually dropped as he fairly gaped at Pike, stunned speechless. Next to Pike’s antigravity chair, Spock looked down at him, one singular pointed eyebrow raised in what Pike could guess was a mild version of shock. Seated at the table by the viewport, Tron regarded him with a sense of confusion instead.

“Those files were supposed to be restricted?”

“With the highest encryption, backed up by multileveled security clearances, which with a civilian login like yours, you shouldn’t even be able to see them.” Pike watched with mild amusement as Tron’s usually blank features turned contemplative. Sam was still in shock.

“Oh. I see.”

“Tron, you hacked Starfleet Intelligence?!” Sam’s voice was at least an octave higher than usual, which made Pike want to laugh; it was like watching McCoy and Kirk from their Academy days all over again.

“So it would appear.”

A strangled noise escaped from Sam’s throat as he stared at his partner. “...How even-!”

“Actually, I would like to know the answer to that question as well,” Spock said, clearly impressed even if his tone was deceptively mild.

“Yes, how about a little demonstration, Tron.” Pike asked, although it was clear that it was more of an order. The program shrugged in response, bringing his little PADD over to Pike, dragging a chair with him.

He sat down next to Pike, with Spock looking over his shoulder and started paging through the different file libraries, starting with publicly accessed libraries, but he showed the path he typically went through, and it was once he tabbed into the first restricted library that Pike caught on to what was happening; every time the program accessed a file that went beyond his civilian clearance codes, his hands and fingers started glowing just the faintest bit blue against his skin in patterns that resembled circuit boards and digital pathways.

Tron was somehow bypassing all electronic security as easy as he breathed, doing it subconsciously and completely organically.

“You’re a security program, a watchdog program specifically designed to monitor the entirety of a system for any illegal activity, so it would stand to reason that computer security would be no obstacle for you, especially if it’s a part of your… unique digital-biology.” Pike was equally impressed and intimidated; it was a very good thing that Tron was on their side - or rather, on Sam’s side. He had a feeling that if they turned Sam against the Federation, they would disappear and never be found. It would be a very good idea to stay in Sam Flynn’s good graces, which worked with Pike’s plans, as the Enterprise and her crew were some of the best recruiting materials he had. “I’ll have to brief SI about you and the nature of your existence, so until then, could you lay off the restricted files until I can generate a specialized identification for you? I would hate to have them all in a tizzy over nothing.”

The program shrugged, nonplussed with the request. “Of course. I apologize for the inconvenience. In the meantime, I’d like to take you up on your previous offer of legitimate Starfleet credentials, since you’re here.”

Pike smiled broadly, suddenly ecstatic; Tron would make an excellent officer for Starfleet. “I’ll send you a list of Academy courses and tracks, so you can decide what to apply for. You two have a good day.”

“Tron, if I may, I would like to discuss your abilities with you in detail at a later time.” Spock said as Pike maneuvered his chair towards the door. The security program nodded, looking forward to it.

“Of course.”

“Yeah, see you guys later,” Sam said, still bewildered at the unusual chain of events. “Tron, we gotta talk about...”

The door slid shut behind Pike and Spock, cutting off the rest of Sam's voice and the rest of whatever he was going to say, clearly a chastisement of some sort. In the corridor, Spock glanced down at Pike, noting the wide grin on the Admiral’s face. “You are pleased with this outcome, Sir?”

“Of course, I am, Mister Spock; I think this is brilliant.” The Admiral’s grin widened, clearly amused. “These two, and whoever else they bring out, will change everything, in ways that we can’t even begin to imagine. Have McCoy do some testing on Tron, with his consent, of course. We need to know what these programs are capable of.”

“Understood, Sir.”

* * *

It doesn’t take more than fifteen seconds after surfacing from the medically induced coma after his surgery for Sam to be utterly and completely bored, even if he can’t string two brain cells together long enough to think. He’s still fuzzy, foggy from the painkillers and his mismatched memories, but he’s aware enough to know that he’s no longer inside the Grid. Even with the heavy duty painkillers running through his system, he knew that everything still hurt, but it was more like it was at a far away distance.

“Hey, you finally awake, kid?”

It took Sam longer than he’d anticipated to tear his gaze away from the white ceiling to stare briefly at the person next to him. It took even longer before he recognized the man.

“Hardly call this ‘awake’, Doctor.” He frowned at the slight slur to his words, irritated that his tongue wasn’t working properly.

McCoy snorted inelegantly with a small roll of his eyes. “Yeah, I’ll bet. How’re ya feelin’?”

“...Like I got some major surgery. How bad was it?”

“Honestly, kid; it was kinda hit or miss for a little while. If your Gemini hadn’t given me a crash course in bein’ a User, you’d have died in there, kid.” The doctor started to run a small instrument over his torso, watching the corresponding data on the tablet he held. “I like him; got a good head on his shoulders. Welp, looks like everything’s healing right, and you’ll be stuck in here with me for about a few more days before we can get you situated in your quarters. You’re still drowsy, so feel free to go back to sleep at any time.”

Sam might have made a noise of some kind, but he was already drifting back down into the undertow of unconsciousness.

The next time he woke up, still bored and still fuzzy, Sam was quick to notice that he had a visitor - two visitors, in fact. Tron was next to him, holding his hand gently even as he listened to Jim Kirk speak from a spot closer to his knees, who was going on a tangent about… 19th century British Naval history?

Odd subject, but whatever. To each his own.

His hand twitched reflexively, alerting Tron to his current state of consciousness. The program looked down at him, smiling gently as he realized that Sam was actually awake, stroking a thumb over the back of Sam’s knuckles in an affectionate gesture that Sam adored. “You’re awake. How are you feeling, Sam?”

“Still fuzzy ‘round the edges, but better.”

“Yeah, Bones still has you on the good stuff,” Kirk said with an easy smile. “Glad to finally meet you face to face, by the way.”

“Coulda done the meet-n-greet without the drama,” Sam realized that his response time was still off, likely due to the drugs he was on. “How long have I been under?”

“It’s been about four days since Bones dragged you out of the terminal. If he clears you in the morning, you can rest in your quarters for the remainder of your recovery. You’ll be off your feet on bedrest for at least for another week, maybe two.” Kirk said, his easy smile never fading. “Bones will have more details for you two later.”

“You need to be more careful, Sam.” Tron gentled the small rebuke with a soft shine to his usually intimidating gaze, but Sam was far too used to the program’s intense stare. Sam squeezed the hand holding his in response, acknowledging Tron’s concern.

“‘S’not like either of us planned on an ambush, Tron,” Sam grinned at his partner, the expression a little loopy from the painkillers in his system. He shifted his head to include the Captain in the conversation. “So what happens now?”

Kirk shrugged and casually crossed his arms across his chest, seemingly unconcerned. “Well, for us, we continue as planned; we’ve had a few glitches down in Engineering, stalling the ship’s departure for our mission, but we should have that ironed out in no time. For you two, just relax. My Communications officer, Nyota Uhura, seems to have adopted Tron - and by extension, you too, so expect a visit or two.”

“Who knows the truth about us?”

“On the Enterprise, just the senior bridge staff, but also my Chief Engineer; you met him briefly during that vidcall. On the Starfleet HQ side of things, only a couple Admirals know, including Pike and Archer, who’s an awesome guy, by the way.” Kirk grabbed a small tablet that had been left on a small table next to Sam’s bed, tapping at the screen. “We’ve relocated the Grid Terminal down to your quarters, although Bones wants another chance to talk to someone called Gemini?”

“He’s my Admin program; Doctor McCoy met him on the inside.”

Kirk nodded absently, still tapping away at the screen of the tablet. “Yeah, Bones said his help was invaluable down there. Is there anything I can do to make this easier for you? I know the painkillers Bones has you on right now are still a little strong, but if you’re anything like me, you’re gonna be bored out of your mind on mandated bedrest.”

It took Sam a few minutes to parse through Kirk’s words and formulate a response because his brain was still a little slow for the time being. “Um, honestly, probably just something to read to start. I don’t think I’ll be up for my normal hobbies for a while.”

“What did you like to do? I mean, back before this all happened?”

“Programming and designing, mostly. I designed a lot of things for Encom, from software to gadgets. I had a sweet Bugatti motorbike, too, that I practically rebuilt from scratch. Honestly, I was kind of a nerd; studying a bunch of different fields after my dad died, because I wanted to make a difference and the grid was my key for that. Before, I was kinda lost; I didn’t know what to do with my life outside of getting in fights and generally causing trouble.”

Kirk looked down at his lap, his easy smile now a self deprecating smirk. “It’s amazing how similar we are, you know that?”

“... How do you mean?”

“My father, George Kirk, became Captain during an attack on his ship, and twelve minutes later, he died saving eight hundred lives, including that of his wife and his newborn son. I lived under that shadow doing nothing good with my life because how could I live up to that? Pike recruited me in the end, and Starfleet changed my life.”

Sam knew what he meant, knew how he felt. He could easily see the parallels between their lives; troubled childhoods after their fathers vanished from their lives, leaving behind a legacy almost too grand to live up to; kids too smart for their own good, getting into trouble far too easily; and an event that changed the course of their future… for Kirk, it was successful recruitment into Starfleet and whatever events lead to his Captaincy, while for Sam it was the discovery of the Grid and his father and Tron.

Jim Kirk was a kindred soul for Sam, and Sam knew right then that this was a friendship that would last for years to come.

“So how about when I’m back on my feet, you and I go hit up a bar and share some stories? ‘Cuz I bet you’ve got some great ones.”

Kirk laughed, blue eyes glittering with delight. “Hell yeah, I do! I’ll even buy the booze!”

Tron glanced between the two of them, a hint of trepidation and something like dread steeling in the shadow of his eyes, sparks flashing. “I’m going to regret this epic friendship, aren’t I?”

Sam locked onto Kirk’s dazzling blue eyes, mischief bright like the sun behind a supernova smile, and the two of them started laughing hard enough for Sam to clutch at his wounded torso.

He also wasn’t surprised when McCoy burst into the room and chased Kirk away with threats and gruff attitude before stabbing Sam in the neck with what he learned was called a hypospray, the drug cocktail inside soothing his stinging wounds and sending him back down into the inky realm of forced sleep, but Sam didn’t mind so much.

Things were starting to look up.

* * *

Because Sam was going absolutely stir crazy only two days into his mandated bedrest, and annoying Tron along with him, McCoy allowed the User to explore the Enterprise on the sole condition that he be escorted by his security program partner with his butt firmly parked in a state of the art antigravity chair and his casted leg secured in place.

Sam agreed to the condition before the good doctor had even finished laying down his version of the law, which just made McCoy snicker and Tron grin.

And so it was that found the pair of them in one of the observation lounges on the starboard side of the beautiful starship, mostly empty except for a few junior officers occupying a table on the far side of the room, while Tron led Sam to a spot by one of the large windows with a stunning view of the earth gently spinning below them with the moon nearby.

It was so heart wrenchingly beautiful that Sam felt tears gathering and his breath caught in his chest.

It was there that some of the bridge crew found them, with Uhura leading the small pack with a gorgeous smile as she led Sulu and Scotty over to the civilian pair, waving to Tron as they approached. The security program nodded in acknowledgement and gently nudged at Sam’s shoulder to gain his attention.

Sam reluctantly tears his gaze away from the stunning view of his home planet (and what a phrase that is) to watch the approaching trio, warmed by the smiles the unknown man and woman are giving his partner. Tron had told him briefly of the crew members he’d met while he had been rushed off into surgery, and it was encouraging that they’d been welcomed with such care by complete strangers, especially given his recent past.

“Tron! How are you doing?” The woman Uhura, with beautiful dark and smoky skin and a high tail of smooth dark hair, highlighted by her red uniform, swept the program into a welcoming and warm hug, arms wrapped around his shoulders as though they had been fast friends for years. She turned her brilliant smile on Sam and gave him the same treatment, welcoming Sam into her life with a warm hug that greatly reminded him of Quorra’s affectionate attitude. “And you must be Sam; I have heard so much about you.”

Sam laughed lightly, giving her a charmingly crooked smile. “Now I’m scared to ask!”

Uhura swats at his shoulder, a light and delicate touch due to his healing injuries, returning his grin with one of her own. She claimed a chair across from Sam and Tron, the two men with her claiming a small couch perpendicular, both of them with warm welcoming smiles for the two civilians.

With formal introductions made, conversations welled up with a natural ease as Scotty engaged with Sam about the technology of the laser and the Grid that had housed him for more than two centuries, the two men talking faster and faster with more complicated vernacular and engineering terminology passing between them with each passing phrase. Uhura made the odd comment, easily following the debate that would have surprised Sam had he not realized that, clearly, the crew of the Enterprise was staffed almost entirely by geniuses - it was not at all surprising that while Uhura was a gifted prodigy with languages, she thoroughly enjoyed the challenges presented by mechanical engineering.

Tron and Sulu quickly entered into a debate on life inside the Grid and of TRON City, the pilot curious about the type of life inside a computer, if they had a form of plantlife (no, not like on the outside, but it wasn’t beyond the realm of possibility, which absolutely delighted Sulu), which in turn led to a spirited conversation of daily life for programs, which drew Uhura in as well.

No one batted an eye as Tron kept close to Sam’s side, a possessive yet affectionate hand touching whatever it could (arms, shoulders, back) or when the two civilians would give each other soft and gentle looks, love and tenderness clear on their faces.

Personally, Uhura thinks they’re just darling together, and teases Sam just like she would her brothers, pleased with the almost shy responses she gets in return.

Later, after shift changes, the small group is joined by both Kirk and Spock, the Captain joining the conversation saturated with mechanics and design with Scotty and Sam, while Spock opted for a game of chess with the security program, a delighted Sulu and Uhura watching in the wings as the program picked up the intricacies of the game with an astonishing speed, making each match an exciting challenge.

Later, sometime after McCoy has joined them, Sam breaks away from his fellow gearheads to look upon the people surrounding him, and for the first time in a long time, he feels safe and accepted.

It was also hard, because he missed both Quorra and Alan fiercely, and he wished that Gemini was here too, but he felt that maybe this was what it was like to finally have a family.

It was just the start of a family, anyway, but he still felt that hope in his heart, and he knew he would fight tooth and nail to keep this dream alive.

* * *

It was two days before the Enterprise was set to depart from spacedock, and McCoy had already released Sam from his Medbay on firm orders of bedrest. Currently, he was just finishing up some last minute paperwork that needed his signature and sign off before the ship’s departure, so he was ensconced in his office, glaring halfheartedly at the documents that seemed to multiply in triplicate with every form he signed and sent off.

This was the part of the job he hated, but damn if he was gonna step down and allow some incompetent boob take over his job. No, McCoy was the best CMO in the ‘Fleet, and he knew it, so he put up with the less satisfying aspects of the job.

His inbox pinged with a new message, so McCoy took the chance to get away from the drudgery, reading the short missive from Tron, of all people. The message was short, terse and almost panicked, so McCoy invited the program to his office to talk in person.

It wasn’t long before the security program was walking through his office door, and the doctor motioned him to the empty chair on the other side of his desk. “So what’s bothering you, kid?”

Tron stared at him, features carefully blank, but there was something in that intense stare that told McCoy that the program was highly concerned. The program placed his PADD on McCoy’s desk, the screen showing reports that the doctor was already familiar with - he’d written some of them after the Khan Incident.

“It took some digging, but it ultimately wasn’t hard to discover and extrapolate that the likely cause of the Augment movement two hundred odd years ago was the discovery of biodigital genetics and the manipulation of what was termed Isomorphic algorithms found in a single source. Yes, records are sketchy or missing altogether, but what Sam has shared with me about his genetics research with Quorra and the timing of your Eugenics Wars leads me to the conclusion that Sam’s work was the cause of such devastating events, ending with was is being called the Khan Incident by Starfleet.” Tron’s intense gray gaze shifted into something terribly sad and tragic. “This is going to devastate Sam, this will break his heart.”

“Why do you think it was Sam’s genetics research that caused those conflicts?” McCoy asked, leaning forward to place his arms on his desk, glancing through the documents that Tron had put together. As he read through the scientific documents, he saw the timeline the program had put together, and if he was honest with himself, the time did fit with Sam’s disappearance and what little they knew about what Encom had been doing in that time period. “Besides, without Khan, I never would have been able to bring back Jim.”

“That is the only positive thing I can see, although I do not fully understand the intricacies of everythingI have discovered.” Tron sighed, the sound punctuated by the faint ever present purr in his voice. “But to answer your query, the answer lies with Quorra.”

“And who is Quorra?”

“Gemini gave you a brief history of the recent troubles within the Grid, so you heard him mention the programs called ISOs, correct?” Tron waited until McCoy nodded before continuing. “Quorra was the last of the ISOs, and during Sam’s first visit to the Grid, she left with him; her very survival depended on it, as CLU and his forces, myself included at the time, would have killed her on sight. The ISOs were different from the basic programs, evolving into creation spontaneously, and their digital DNA was unlike anything seen before, and unique because of it.”

“Gemini did mention that, yeah.”

“According to Sam, they were starting to gather data about the differences between Users and ISOs on the molecular level, using samples of Quorra’s DNA. She died that night that Sam and my User, Alan-1, fled from Encom and the coup. She managed to destroy the original research that night, but I wonder if…”

“You think the bastards that killed her used her body to conduct their own research, thus the small gap in years from Sam’s disappearance to the approximate start of the Eugenics Wars,” McCoy voiced the conclusion that Tron had come to with his research. He also agreed with Tron; This would devastate Sam.

“Yes, I do.”

McCoy nodded, mind racing as he started to plan for inevitable therapy sessions that he could see was in Sam’s future - Tron’s future, too, as the program was distraught over the discovery, even if he hid it incredibly well. Being a Program, although changed on a genetic level from what he understood, Tron had cause to be concerned of ending up exactly like Sam’s friend - dead and dissected in a lab.

Sam was going to be devastated that everything good that he had been working so hard for had been corrupted and destroyed, and if he was anything like Jim (and he was, scarily so) Sam was going to feel incredible amounts of guilt and self-loathing at not being able to prevent those events from occurring. McCoy knew that it was the actions of people far beyond Sam’s control that had caused the tragic events, but Sam would still feel responsible for them.

“Look, this is gonna be a long term problem that we’re all gonna have to deal with, but one thing that I can personally guarantee is that whatever happened to Quorra is not going to happen to you.” McCoy held Tron’s stare as he spoke, relieved to see some of the tension easing. “I will not allow it; we would send you two back inside the Grid first and destroy that laser, so that no one would be able to get a hold of you or Sam.”

He knew his heartfelt words had an impact, as Tron appeared almost stunned by the ferocity of his statement. To him, though, it was just a matter of fact; he would protect Sam and Tron, and everyone else inside the Grid from being used by anyone, even if he had to steal the Terminal and run to the edges of the universe to do it.

He was positive that Jim would protect them just as fiercely, too.

“Also, we’ve got time before we tell any of this to Sam, because unloading all of this on him now would be detrimental to his recovery. Luckily for him, and you, I have the background necessary to act as a kind of therapist, so we can talk through all these issues that I’m sure are going to come up from this.” McCoy leaned back in his chair, grabbing a spare PADD from his desk to start organizing the beginnings of future sessions.

“Why me?” Tron’s features took on a quizzical cast, even as his stare was still as intense. “

Well, for starters, I can infer that your past has left some pretty intense trauma to your psyche, even if I don’t know the details. Some of Sam’s trauma coincides with yours, so we’ll be learning to deal with that in a healthy manner. You’re also incredibly co-dependent on Sam, just as he is with you, which isn’t necessarily a bad thing, but it could become a problem later down the line.” McCoy watched as Tron processed his words, confident that the program would see his logic. “There’s also the fact that you’re going to be learning what it means to be human, which is what you’re classed as on this side of the Grid. That, in and of itself, is cause for some therapy, and is incredibly common for the rest of us, too.”

“...I see.” Tron had turned pensive as the possibilities of his future crossed his mind. “Thank you, Doctor.”

“Just doin’ my job, Tron, but you’re welcome.” McCoy paused for a second before reaching for his computer. He brought up a few files, transferring a copy to Tron’s PADD and handing it back to the program. “There is another matter that I think you can help me out with; I was going to wait for Sam’s recovery, but maybe you could help instead.”

“How so?”

“Well, when we found the Grid terminal, we didn’t find only the laser and terminal; we found a body, too.” It was fascinating to watch as Tron made the obvious connection, even with only the scrap of information that McCoy provided. “Based on Sam’s description of the night he came to be inside the Grid, and our own research and testing, I’m fairly certain who’s body I have in my morgue, but confirmation would always be welcome.”

“...Of course. If it is who I believe it is, Sam would want to see him, too,” Tron seemed a touch unsteady, which wasn’t surprising to the doctor, considering who it was that had created Tron so long ago. “May I ask how he died?”

“From what we could infer, there was a fight of sorts, and he died from several shots to his torso, leading to a quick, if painful death from blood loss. He collapsed the building and the stairs leading to the room where the terminal was kept, keeping you hidden from the rest of the world. If I’m being honest, he died a hero, sacrificing himself to keep Sam safe.”

“...I wish I could have met him. To meet your Creator-User... “ Tron trailed off, looking bereft. He reached for his PADD, undoubtedly to read through McCoy’s report of the corpse, which included a composite sketch of what the dead man would have looked like alive, and an ancient copy of an employee ID picture. With a look of surprise, Tron blinked away unshed tears as he stared at the picture of the man who’d created him.

“I do look like him… Flynn always said that we looked like our Users; Gemini is proof of this, even though there are obvious differences. I never realized we would be identical.” Tron tore his gaze away from the pictures displayed on the PADD to stare at McCoy intently. “This is Alan Bradley, my Creator-User, although I knew him as Alan-1.”

“I thought as much. We can talk Sam later about funeral arrangements and what to do with the body, unless you had any ideas?”

Tron shook his head in the negative even before McCoy finished the question. “No, programs don’t die in the same manner that Users do. You saw that inside the Grid.”

“Fair enough. Why don’t you go and get some rest, okay, Tron?” McCoy rose to his feet, the security program doing the same. “We’ve just talked about a lot of pretty heavy stuff; it wouldn’t be a bad idea to take some time and allow yourself to process everything.”

Tron left McCoy’s office soon after and the doctor returned to his paperwork. He sighed heavily as he thought about the implication of Tron’s research and felt saddened by the events revealed to him. The idea of Sam’s friend being defiled for base experimentation that eventually led to the kind of genetic engineering of the Eugenics Wars and the rise of Khan and his army of Augments was depressing.

Actually, it was _beyond_ depressing.

He had a lot of work ahead of him, in order to make sure that both Sam and Tron (and hopefully Gemini, too) acclimated to this new world of theirs in a healthy manner, and he was not above wrangling help from Jim and Spock and the rest of their modge podge family of genius misfits.

The next five years were certainly going to be… interesting.

Somehow, feeling a sense of excitement he usually attributed to Jim, McCoy couldn’t wait for the fun to start.


	9. Chapter 9

**Notes for the Chapter:**

> So, that tentative timeline of a couple weeks at most to write this thing? Yeah, that turned out to be a lie...
> 
> I struggled a lot with this chapter, and now that I've finished it, I've no idea how. Life interfered, writer's block, depression, the usual excuses.
> 
> I've got plans to actually finish this fic, I want to finish this, so badly, it... just might take a while.
> 
> Also, these character development and world building scenes are not strictly laid out in a linear fashion, but they do all happen in the same 10 week period.

**_4 weeks after leaving the Grid_ **

“Doctor McCoy, you wanted to see me?”

McCoy looked up from one of the end-of-day reports he was reading through, one of several that needed his signature before being filed away. He had asked for this appointment with Tron specifically for after his usually scheduled office hours, to be well away from any of the usual prying eyes of his gossipy (but very competent) nurses. “Yeah, I did. I thought it was past time to get you checked out, medically, I mean.”

Tron followed as McCoy led him to a more private examination room, turning the glass opaque with a touch to a panel by the door. “Is it that important? Sam can repair any damage or systems infection through my disk.”

“Sure he could, but you don’t have your disk right now, do you?”

Tron paused, tilting his head curiously as though the thought hadn’t occurred to him yet; it likely hadn’t, what with all the excitement of being in this strange User world wrought. “I see you point.”

McCoy gave a huff, amused. “I bet. So without access to the Grid or your disk, anything that happens to you is my responsibility,” He motioned for Tron to take a seat on the exam table, grabbing a tricorder and a couple other diagnostic tools from the designated cabinet. “In order to do that, I need to know what makes you tick.”

Tron nodded and obeyed the doctor’s silent commands, settling himself without complaint. “What’s involved with the process?”

“I’ll just be taking a couple in depth scans; nothing painful or incredibly invasive, if that’s what you’re worried about.” McCoy started his initial scan, right at the top of Tron’s head and working his way down the program’s body slowly with the scanner, with a hum of satisfaction at the results. “So far, it looks like you’re physically the same structure as humans; organs, bones and the different systems - from the musculature to the respiratory - but your capabilities might be more on par with those of Vulcans.”

Tron hummed in approval, having already read about the species. “They are a fascinating species, to be sure.”

“How does that compare to how programs are inside the Grid?”

Tron took a few moments, more to formulate his response than anything else.

“In comparison to Users, most programs are several times stronger, faster - just _better_ , but not necessarily smarter, as we are often confined to our programming. We are also not quite as bound by the constraints of the laws of physics, for example. It would be interesting to see how a Vulcan User would fare, and what a Vulcan Program would be like. But for all of our advantages, Users are gifted with the power to change the world as we know it, as you saw when you came into the Grid. Programs cannot do the things Users can so easily; we cannot change the fabric of our reality.” Tron sighed, showing a small amount of melancholy. “To know that in this world, programs are basically the same as Users is… surreal at best.”

McCoy allowed the following silence to stretch as he read over the results of his scan. For a being that had only effectively been alive for less than a month in the more conventional sense he was used to, Tron was in excellent physical shape, although his scans also read like those of a newborn`; McCoy was going to have to give a couple rounds of the standard vaccinations and immunity boosters, just to be on the safe side of things. He wasn’t even sure yet if programs _could_ catch organic diseases, but he wasn’t about to take that on chance and luck.

“So, just as a head’s up, I’ll need to take a sample of your blood, for testing purposes,” He raised a hand to forestall any of Tron’s protests, knowing the security program had them especially after their last rather heavy discussion about Quorra. “It’s purely investigative for medical purposes; I’ll be the only one to handle the samples, and I’ll either destroy them afterwards, or, and this is depending on what I find, I’ll be the only one able to access them.”

“... What are you hoping to find?”

“I want to find out if you’re as vulnerable to external forces as we are; for example, allergies are like glitches in our genetic makeup, where certain substances will cause our bodies to overcompensate at best and destroy itself at worst. I’m sure that by now, you’ve read Jim’s medical file?” McCoy had been briefed by Spock on Tron’s natural (freaky) ability to bypass security measures, so he felt it was a given that Tron had likely read all of the personnel files from the Enterprise, at the very least.

“Yes.”

“Due to the unique circumstances of his chaotic birth, he ended up being allergic to practically half of known medicine and a crazy amount of different foods, which affected his diet and nutritional intake as a kid.” McCoy placed a hypospray to Tron’s arm, withdrawing a sample of his blood. “He did alright, considering, but after the transfusion with Khan’s blood (incidentally a universal donor) that saved his life, the new blood also wiped out all of his allergies. Not only that, but now Jim’s got a stronger resistance to all known diseases, too.”

“And you wish to test if I have similar properties, considering my theory about Quorra and the rise of the Augments.”

“Exactly.”

“And it would be for your eyes only?” McCoy grinned reassuringly, lightly dropping a third vial of blood onto a little tray table. “Of course; although, if you consent to it, I may have Sam take a look at the samples, too, or at least the results. I’d like to know if there are any similarities between his old research and what we can find out with your samples.”

McCoy’s exam took about an hour, during which he determined that Tron was, essentially, just a better human, although with a much stronger electromagnetic field than the rest of the species, which considering his origins as a Program, wasn’t at all surprising. It would be something to watch out for in certain environments, much like someone with a pacemaker needed to be a little more cautious.

He doubted that there would be any concerning anomalies in Tron’s bloodwork, but he would consult with Sam on the results. He decided that he wouldn’t work with the precious samples while anyone else was in his Medbay, and he created a secret file hidden behind the security lockdown on Jim’s files to store the data (and Gemini’s, too, when he had it).

Besides, apparently only Tron could get past the security on Jim's files, so it'd be the perfect hiding spot.

* * *

**_6 weeks after leaving the Grid_ **

By the time McCoy was satisfied with how Sam’s injuries were healing after his rather intensive surgery, Sam was practically climbing the walls. He’d always been one to have a couple of projects to keep himself occupied, whether it was running Encom or tinkering with his bike or doing some extensive coding, or even working out.

To be stuck on bedrest (even though he had been granted one or two short excursions already), unable to move from the admittedly comfortable bed, made his skin crawl from the inevitable restlessness. His only option to pass the time was to read or watch holovids (some were awesome, and some were awful).

Sure, he had a lot to catch up on, and had already made considerable progress (not even remotely as fast as Tron was going with his own personal studies), but there was really only so long that he could stare at a screen before his mind rebelled, no matter how interesting the subject matter was.

He’d at least caught up on Galactic History, which had been both fascinating and enlightening.

McCoy had also vetoed Sam doing any work on the Grid, at least until he could move around without aggravating his healing body.

And he couldn’t keep Tron confined to their quarters with him to keep him company, it wasn’t at all fair to him, especially with the new friends he was making.

They were fast becoming his friends too, as they all visited him just as much as they saw Tron, taking time out of their limited off shifts to check in on him and Tron both. Sam greatly appreciated the gestures, even if he chafed a little at his own lack of usefulness.

Still, he damn near cried when McCoy walked into his quarters pushing an advanced (to Sam) wheelchair, his medical bag slung over one shoulder. The good doctor caught his overjoyed expression and snickered, the look taking years of stress off his face.

“I take it you’re happy to see me?”

“Doc, you have no idea just how happy I am to see you! I mean, sure, these are nice enough rooms, but goddamn I am close to losing my damn mind. A change of scenery will really help me out.”

“I’ll bet. Now, I do wanna give ya another checkup before I get you squared away in the chair, see how things are doing.” McCoy kept the chair to the side as he checked over Sam’s healing limbs, lightly massaging the flesh as blood flow returned to normal and easing his spasming muscles with a deft touch, agitating the pins-and-needles feeling spreading fast up his leg, drawing a muttered curse from Sam that had McCoy huffing a small laugh at his expense.

“You’re just about as good a patient as Jim is, aren't ya?”

Sam replied with a rude gesture, leaving McCoy to snicker at him.

Almost a half hour later found Sam maneuvering his way through the halls of the ship in his new gravity chair (which had a small learning curve to it), generally trying to keep out of the way of the crew as it was in the middle of Alpha shift. Although, Sam was quickly finding that he was actually getting a bit lost. The halls were just nondescript enough to throw him off, and he had no frame of reference for where anything was, or what department he was currently in, and he belatedly realized that he should have grabbed a comm or something.

The time he spent wandering aimlessly was spent somewhat productively as he already had an idea for his next construction project, if he could find the Engineering department; a HUD visor that fit over his eyes with an attached earpiece to receive transmissions. He was already thinking of holographic displays and a possible AI mini supercomputer, but that part wasn’t strictly necessary.

Eventually, Sam found his way into the Engineering Department, and it felt like coming home, if he was honest with himself. The place was a thriving hive of activity, several levels deep, and the sleek design of what had to be the ship’s engine almost had him drooling.

Scotty caught sight of him almost immediately, waving him over to a workbench with a shout of welcome. “Sam! You have freedom!”

Sam laughed, maneuvering the gravity chair over to the Chief Engineer with a wide grin. “Yeah, about time, too.”

“So, what’s got ya travelin’ down into my territory, lad?”

Sam shrugged with a wry grin. “I was actually hoping to find something to do; I haven’t been able to actually tinker in so long. It’s literally been over 200 years since I was last able to build something with my hands.”

Scotty’s look of sympathetic horror startled a laugh from Sam and the engineer actually stepped backwards with a dramatic hand over his heart. “We cannae be havin’ that! Here, use this workbench; I’ve already got a bunch of tools for ye to use, and I’ll scrounge up a box of scrap parts for you to use at your leisure. You’ve already got some ideas, right?”

“Yeah, I got a couple. If you’ve got some time, I could use a second opinion?”

When Tron found them hours later, he could only watch fondly, leaning against the wall, as Sam and Scotty were neck deep in a variety of little projects; Sam already had his HUD visor working with a second one he was going to give to Tron, and what looked like the beginning processes of a lightsword. Both engineers were currently debating how to create the blade: a metal blade with a laser edge or go straight to a plasma blade?

Tron supposed, in the quiet respite of his own thoughts, that it made sense for Sam to outfit himself with a weapon; their time in the Grid had forced Sam to become quite proficient in using one.

… Maybe he could see if Sam could figure out how to create the equivalent version of Tron’s Disks.

* * *

**_7 weeks after leaving the Grid_ **

Finding out about the details of Alan’s death had been… more difficult to swallow than he’d anticipated, Sam decided, his throat tight and his vision becoming misty as he looked down as what was essentially a pile of bones - all that remained of his mentor and pseudo father.

He reached out and carefully grabbed Alan’s cracked glasses from the autopsy table, keenly aware of Tron at his side, frozen in place with his own conflicted emotions.

“If it’s… any consolation, he died quickly,” McCoy muttered behind the pair, subdued by the occasion.

“What… what do we do now?” Tron asked quietly, ill at ease by the remains of his Creator-User, who was the closest thing he’d ever come to having a deity. He remembered from the old system, where he’d first met Sam’s father, how Users were part of a religion of sorts. That ideaology hadn’t exactly transferred over the newer Grid system, but there had been programs that believed in that way.

To see all that remained of Alan-1 in such a… messy fashion was discomforting.

“You have a few options, to be honest; you can have a funeral or a wake.” McCoy explained with a small shrug. “Funerals in space have a tradition where we jettison the body out into the black, to roam forever onwards like the explorers we are. But I think I’ve got a better idea for you two, since neither of you now Mr. Bradley were spacers.”

Sam looked over his shoulder at the doctor, twisting as much as he could in his wheelchair. “Such as?”

“Since all that’s left are bones, Scotty and I could compress them into diamonds or something similar for you, to always keep him with you.” McCoy shrugged, deliberately casual in a way that wasn’t pity, which both Sam and Tron appreciated. “That way, the two of you have a keepsake.”

It was a good idea. Neither Tron nor Sam had much in the way of possessions in the organic world, except the clothes they wore exiting the Grid, and so this would be a big deal for the both of them, and intimately special and sentimental.

Ultimately, they both decided that there would be no funeral in the usual sense, nor would they want a wake, since only Sam really knew Alan as a person, and while Tron had been built by Alan, he’d never had the chance to meet his Creator-User.

They celebrated his life and his significance in their lives as they designed the keepsake, taking a couple of days to design it together. The design they settled on was a circular disk shape, much like the Identity Disks from the Grid, no larger than an inch that could be clipped onto a chain to wear around the neck, keeping the man’s memory close to their hearts. Sam also took the time to inscribe on the design Alan’s name, his Username, and his dates of birth and death.

Once the design was finalized, it only took Scotty about a day to craft Alan’s remains into a pair of beautiful diamond-sparkling disks, handing them over with a great deal of care and reverence, which caused Sam to choke.

“Thank you, for doing this,” Tron whispered, the words rough with grief and regret.

“Of course, laddie,” Scotty said just as softly, placing a comforting hand on Sam’s arm. “Yer more than welcome.”

* * *

**_5 weeks after leaving the Grid_ **

When Spock walked into the training hall near the Security department barracks, the last thing he was expecting to witness was the Program Tron throwing his current opponent into a wall, the unfortunate Secops officer collapsing with a thready groan. He did not get back up; instead, he slowly crawled to support himself on the wall, grimacing from pain.

Two full teams of Security officers were in similar positions along the benches near the equipment on the far side of the room, cradling sore limbs and attempting to massage aching muscles.

Spock turned his unflappable gaze from the downed officer to the Program in the middle of the large and open room, raising one eyebrow delicately in question.

It was only his greater observational skills that allowed him to see Tron’s satisfied smirk, the microexpression appearing more as a feeling and an electric glint in his cool grey eyes.

“Are the onboard facilities to your liking?”

“Adequate. Different,” Tron gave a small shrug, posture relaxing as Spock approached. “The men are good, for baseline humans. A little limited, compared to even the most basic programs, but still good.”

“And what of your own capabilities?”

“Mostly on par to my home environment, minus some of the more gravity defying acrobatics,” Tron’s smirk visibly grew as he appraised Spock as he ran through his warm up routines. “Maybe a different species will provide more of a challenge?”

The shadow of a smirk graced Spock’s mouth, his dark eyes suddenly predatory in a way that made Tron’s grin widen further. The tension in the wide open room thickened sharply as the exhausted Security forces caught on to what was about to happen. Spock graciously decided to ignore one of the assembled officer’s attempt at subtlety and pretended not to see the holorecorder.

“You seem confident of yourself.”

“I am firmly aware of my own skills.”

Spock dropped into the opening stance for Suus Mahna, the ancient Vulcan martial art he was very much highly proficient in, and waited for Tron’s opening move. He noted how the Program’s fists were clenched as if holding one or more weapons.

“You are used to fighting with weapons.”

“I’m used to fighting with my Disks, which, technically, are the same thing. It won’t be a problem.”

“We shall see.”

Tron started the spar with a lunging punch, inhumanly fast, following with an aerial kick as Spock dodged out of the way of both moves, retaliating with a kick of his own to Tron’s chest that was just as neatly dodged with a unique acrobatic twist that baseline humans would be hard pressed to perform. Spock twisted into another snapping kick to the other’s chest and head, but Tron grabbed at his ankle and twisted the Vulcan off his feet. Spock followed the momentum with another kick, this time successful as Tron fell back with a grunt, but he regained his stance with a backflip easily.

Spock followed after him, striking hard and fast with knife hand strikes, impressed as all of them were skillfully parried. He blocked a powerful kick to the chest with crossed arms but Tron flipped over his head with another kick aimed at his head, which he narrowly avoided by dropping to the floor and sweeping the program’s feet from under him as he landed.

Tron recovered smoothly with a single handed backspring, bouncing on his toes as he leapt forward as he aimed a strike with his fist to Spock’s head. In turn, Spock grabbed Tron’s wrist and pulled, throwing the program off balance as he simultaneously leveled his knee into Tron’s flank with enough force to break a baseline human’s ribs.

Tron grunted from the force but seemed otherwise unaffected by the blow.

Instead, he grinned and contortioned his body to twist his leg around Spock’s shoulders, maintaining the momentum and throwing Spock into the air to create some distance between them. Spock managed to recover in a roll that allowed him to regain his feet as he eyed Tron with a surprising amount of competitive aggression.

The spar continued in a similar fashion for well over an hour, with neither opponents backing down from the challenge. Their enraptured audience had also grown throughout the course of the fight, including several of their friends; Spock had even glimpsed Nyota among their numbers, before the momentary distraction had cost a blow to his face, resulting in green blood flowing from his nose.

He repaid the blow with one of his own, his foot breaking the skin across Tron’s brow, allowing bright red blood to flow free.

Neither of them were unscathed at this point, both of them sporting a variety of minor abrasions and injuries, their clothes were similarily scuffed and torn, and both were going to be sporting colorful bruises for days.

Throughout the spar, Tron had displayed incredible acrobatic abilities, the motions smooth as silk as he danced around the room, seemingly unhindered by the normal constraints of gravity and physics, piquing Spock’s curiosity about what a fight would look like inside the Grid.

“Alright, alright! Let’s call this ridiculous display a tie and be done with it!”

Both Spock and Tron startled and dropped into more relaxed positions as Dr. McCoy burst into the training hall with his usual flair of dramatics, a large medkit hanging off one shoulder. He ignored the protests of the crowd, scowling fiercely at the louder onlookers, silencing them with a look that promised a slow torture during the next round of physicals.

As the irritated doctor began patching them up, Spock offered to train with Tron whenever he wished, much to McCoy’s dismay, fairly radiating contentment as the Program readily agreed to the offer.

Later, Spocked downloaded the vids of their spar from the Enterprise’s crew forums for his own personal perusal. He also made a note to send the vids to his father for assessment; while his father was ever the diplomat, Sarek would be fascinated with Tron, and would also be pleased with Spock’s use of Suus Mahna against a foreign opponent, even if the outcome was technically a standstill.

* * *

**_9 weeks after leaving the Grid_ **

“Got a gift for you, Doc.”

McCoy looked up in surprise from where he was going over (more and never ending) reports, startled at Sam’s appearance at the door to his office. The younger man looked well, a cheeky grin telling McCoy that he’d already been spending far too much time with Kirk; the two of them together were _demons_.

“Oh yeah, kid? And what’s that?” He deadpanned, giving Sam the caustic look his mischievous attitude deserved.

McCoy’s disdain for Sam’s Kirk-like tendencies didn’t even phase the kid, the little shit. The kid wheeled his way into his office and dropped a large PADD next to his terminal.

“Kid, what’s this?”

“That, my dear Doctor, is your very own access to the Grid,” Sam said with unnecessary flourishes. “Your direct line, in fact. Just turn it on, tap the icon, and you’ll be able to message Gemini at any time. It even has vidcall options.”

“You’re a brat, I hope you know that,” McCoy groused, mildly annoyed that his… admiration for Sam’s Program was, apparently, well known enough to get him teased. He usually had more tact for that (he had to, with Jim fluttering around like dome kind of demented bird; the man could never keep his nose out of gossip). “...But thank you. I do appreciate this. Now get the hell outta my office!”

Sam just laughed at him as he left the office with an irreverent wave goodbye, to which McCoy just rolled his eyes heavenward in a prayer for strength and proceeded to ignore the oversized PADD for his actual work related paperwork that still needed doing.

It wasn’t until he was safely locked away in his quarters that McCoy allowed himself to inspect the unexpected gift from Sam. The PADD looked to be a touch screen, about 9 by 12 inches in size and surprisingly much thinner than the standard Starfleet issued PADD, meaning that Sam must have constructed it from scratch.

Guess the kid was maybe getting annoyed by McCoy asking after Gemini so much in the past couple of weeks.

Operating the device was just as easy as Sam said it would be, with a single button to turn the PADD on, and the icon Sam indicated would reach Gemini was a stylized version of the astrological sign, prompting a small grin at Sam’s cheeky cleverness. Taping the icon gave him two options; one to send a written message, likely in case Gemini was actually busy, and the other allowing for video. He chose the first one, just in case.

_/Hello, Gemini. This is McCoy. Sam finally gave me a way of contacting you directly. Please let me know when you’re available, as I don’t want to be distracting you otherwise./_

With the initial message sent, McCoy felt at odds with himself as he waited for a response, almost nervous. Gemini was by far his favorite program, but he hadn’t seen or heard from him since leaving with Sam and Tron two months ago. He knew, through the grapevine, that Sam had restored the time dilation back to default settings, so it had been even longer since Gemini had last seen him.

Yeah, he could admit it, even if only to himself; he was nervous.

A trilling alarm from the PADD had him looking down, and the option to accept an incoming video call was open. He clicked ‘Yes’ and smiled as the familiar sight Sam’s near twin appeared on the screen.

“Hey, almost thought you’d forgot about me,”

“I could never forget you, Gemini. I am sorry it took so damn long to get back to you, though.”

“It’s alright, Doctor, truly. SamFlynn has informed me that you are responsible for the functionality of 1100 crew members, and you’ve had to prepare for a new long term mission. I fully understand.” “Still, I feel kinda bad leavin’ you hangin’, darlin’, even though I only OK’ed Sam to work on his programming last week.” McCoy paused, replaying what he’d just said in his mind, feeling an embarrassed blush creep up.

Now would be a good time for the floor to swallow him up.

On screen, Gemini looked positively charmed with McCoy’s slip up, a delightfully shy smile growing as he relaxed to rest his chin against his palm. “Of course, Doctor. I must thank you for taking such excellent care of my User.”

“Y’know, you can call me Len, if you’d like.”

“I think I would.” Gemini’s coy grin and that soft slant to his eyes made something in McCoy’s chest ache, and he quickly realized that he was going soft for the program.

“So, have you been keeping busy? Sam mentioned that he restored some of the Grid’s previous functionality.”

“Yes, there have been a few more skirmishes, with the other hostile factions hoping to take advantage of SamFlynn’s absence, but I’ve been able to shut that down, with help from the Sirens.” Gemini shrugged casually, like what he’s been dealing with wasn’t a big deal. “I’d like to know more about you, though, and the world you come from.”

“Oh yeah?” McCoy grinned, a warm feeling unfurling in his chest. “What would you like to know?”

By the time McCoy finally called it a night, hours had passed in easy conversation, the topic drifting casually from topic to topic, from daily life aboard the Enterprise to current affairs inside the Grid. McCoy was actually loath to end the call, stalling for as long as possible, and Gemini was more than inclined to let him, informing McCoy without a doubt that he was enjoying their time together.

When McCoy finally quit his dithering and ended the call with a promise to call again soon, he resolved to visit the Grid again, regardless of his irrational worries about the digitizing laser.

Gemini was worth the risk.

* * *

**_8 weeks after leaving the Grid_ **

“Hey there, Nyota. Just finished your shift?”

Uhura smiled warmly as Sam joined her in the mess hall, where she’d been quietly enjoying a cup of Chiraltan tea with lemon. They’d met up several times already now that he had mobility with his chair, and she found that she really enjoyed her time spent with both Sam and Tron.

Tron was a breath of fresh air, highly intelligent in ways unique to being a program, and strangely endearing with his endless questions about human life. She found him endlessly charming when he and Sulu got involved in any conversation regarding biology and plant life in general, and was equally charmed by his surprisingly philosophical debates with Spock, usually on some obscure facet of information he’d hacked into.

She found Sam to be a perfect counter to Tron, and had it not been for their unique and rather tragic circumstances, she would have never guessed that Sam wasn’t anything other than Kirk’s brother: both were geniuses with complicated pasts, and both were incredibly kind and passionate, and very charismatic. Sam seemed a little more shy than Kirk ever could be, but she was also aware that Kirk hid his fears and insecurities behind that bravado.

She took a sip of her tea and motioned for Sam to join her at her table. “Yes, just enjoying a cup of tea. Would you care for some?”

“...If it’s not a bother, I really liked that green tea from last time.”

She smiled at him, already rising from her seat. “Sure thing, Sam. You get comfortable and I’ll be right back.”

It only took her a few minutes to return to her table, but Sam was already tapping away at a PADD she knew he carried everywhere with him. According to Monty (Scotty), Sam’s personal computer carried everything important, from mechanical designs and ideas to the upgrades and patches he was coding for the Grid. Nyota was immensely curious about the digital world, and hoped that one day, she’d be able to go in.

She was patient, though. She could wait.

She set down the new tea next to Sam, her smile widening as the younger man twitched in surprise. “Are you sure you want company, Sam? You seem to have a lot going on already.”

Sam smiled at her, but the look to his eyes seemed a little sad. “Yeah, I’m fine; I’m not working on any designs this time. Doctor McCoy’s given me a bit of an assignment, like unofficial therapy. I understand the need for it, considering everything.”

“And how’s that going?”

“Surprisingly good, actually,” Sam shrugged a bit dismissively, finishing up his sentence before tucking the PADD away in a modified compartment of his antigrav chair. “Basically, anytime I remember the good things about my life before, McCoy wants me to write it down, so that I have a physical reminder that my life wasn’t just one giant crapshoot.”

“For all of McCoy’s acerbic temper, he’s really just a big teddy bear with a heart of gold. He worries after Kirk like that, too.”

“Yeah, and I’m pretty sure he’s got a crush on my Program, Gemini. It’s actually kinda sweet,” Sam grinned like he was sharing a secret of an illicit affair. “And Gemini’s turning out to be a pretty awesome person too, so that’s a bonus.”

“And what’s Gemini like? You said he’s your Program, but I’m sure I understand exactly what that means. Isn’t Tron your Program too?”

“Not really,” Sam shook his head, the motion highlighting the fond glint to his eyes at the mention of the security program. “Tron’s not my Program in the way that Gemini is; I wrote and coded Gemini, while Tron was Alan’s creation. Tron is my partner, my significant other, while Gemini is more like my… child, I guess.”

“I see. So what’s he like?”

“We’re still figuring that out, to be honest,” Sam sipped at his tea as he tried to figure out how to explain it properly. “The first time he stepped out of the tank, he was a blank slate; no personality. He’s learning, though, and it’s fascinating to watch, too. He’s incredibly kind and quiet, like he’s observing the world first. He’s developing a remarkable sense of bravery, but he’s not predispositioned as a warrior, like Tron is. Sassy as fuck, too.”

Nyota laughed with him, delighted. “You sound very proud of him.”

“I am, and I think Bones would be good for him, and him for Bones.”

“McCoy’s a good man. Doesn’t usually get to play therapist to anyone other than Kirk; how’s that working for you?”

“Surprisingly good. I think it’s only really working because Kirk and I are similar enough, and I’m more receptive to it because the good Doctor reminds me a lot of Alan. He was always worried about me.”

“And what were you writing about now? If you don’t mind my asking,” Nyota asked gently, taking a delicate sip of her tea, pleased when Sam did the same.

“Actually, I was thinking about how Quorra would have loved being here; her enthusiasm was… infectious.”

“Tell me about her?”

“She was… amazing. She was brilliant, and you couldn’t help but be happy in the face of her joy for - everything. She had such childlike curiosity about everything; she had so many questions about everything. The only reason Alan even believed me about the Grid was because of her,” He reminisced softly, his voice a mix of love, grief and wonder. “You’ve met Tron; there’s no mistaking him for human, no matter how much he looks like one. Quorra was the same way, she had the same intensity.”

“She sounds amazing; why didn’t anything develop between you two? It sounds like you and she were compatible.”

“Oh, don’t get me wrong, she was gorgeous,” Sam blushed a bit, just the tips of his ears (Nyota thought that was precious) and his smile turned shy again. “I thought about it at least once in the early days. But my dad practically raised her when he disappeared, and she ended up filling the sister role that I didn’t realize I’d always wanted.”

“Well, I’m officially adopting you as one of my brothers,” Nyota teased, drawing a surprising giggling from Sam, which delighted her further. “So as your older sister, I’ve got to ask: what’s it like to be in a relationship with Tron? Was it love at first sight?”

Sam laughed, bright as the sun. “How do we even know you’re the older sibling?”

“Because I said so! And answer the question!”

“Well, I can tell you right now that it was _not_ love at first sight,” Sam said with a dramatic flourish, rolling his eyes in a way so similar to Kirk that Nyota had to blink in surprise. Sam then told the story of his excursion into the Grid, including the gladiator-style Games and the subsequent meeting of Tron, CLU and Quorra. She listened as Sam recalled the flight towards the portal, and Tron’s reawakening and sacrifice, as well as Alan’s final request before his death. Sam explained how much of a support base Tron had become once he’d repaired him, and Nyota could easily see the transition of feelings from platonic to romantic.

It was incredibly sweet, and she decided that if anyone deserved that kind of happiness, it was Sam and Tron. They were good for each other, she’d seen that already, and she would doall she could to foster that happiness. Sam (and Tron) clearly needed someone to look out for his happiness and well being, and she was prepared to step up to the challenge; she’d let Kirk and the others challenge Sam and Tron in other ways.


End file.
